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Ochs-Balcom HM, Preus L, Du Z, Elston RC, Teerlink CC, Jia G, Guo X, Cai Q, Long J, Ping J, Li B, Stram DO, Shu XO, Sanderson M, Gao G, Ahearn T, Lunetta KL, Zirpoli G, Troester MA, Ruiz-Narváez EA, Haddad SA, Figueroa J, John EM, Bernstein L, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Mancuso N, Press MF, Deming SL, Rodriguez-Gil JL, Yao S, Ogundiran TO, Ojengbede O, Bolla MK, Dennis J, Dunning AM, Easton DF, Michailidou K, Pharoah PDP, Sandler DP, Taylor JA, Wang Q, O’Brien KM, Weinberg CR, Kitahara CM, Blot W, Nathanson KL, Hennis A, Nemesure B, Ambs S, Sucheston-Campbell LE, Bensen JT, Chanock SJ, Olshan AF, Ambrosone CB, Olopade OI, the Ghana Breast Health Study Team, Conti DV, Palmer J, García-Closas M, Huo D, Zheng W, Haiman C. Novel breast cancer susceptibility loci under linkage peaks identified in African ancestry consortia. Hum Mol Genet 2024; 33:687-697. [PMID: 38263910 PMCID: PMC11000665 DOI: 10.1093/hmg/ddae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Expansion of genome-wide association studies across population groups is needed to improve our understanding of shared and unique genetic contributions to breast cancer. We performed association and replication studies guided by a priori linkage findings from African ancestry (AA) relative pairs. METHODS We performed fixed-effect inverse-variance weighted meta-analysis under three significant AA breast cancer linkage peaks (3q26-27, 12q22-23, and 16q21-22) in 9241 AA cases and 10 193 AA controls. We examined associations with overall breast cancer as well as estrogen receptor (ER)-positive and negative subtypes (193,132 SNPs). We replicated associations in the African-ancestry Breast Cancer Genetic Consortium (AABCG). RESULTS In AA women, we identified two associations on chr12q for overall breast cancer (rs1420647, OR = 1.15, p = 2.50×10-6; rs12322371, OR = 1.14, p = 3.15×10-6), and one for ER-negative breast cancer (rs77006600, OR = 1.67, p = 3.51×10-6). On chr3, we identified two associations with ER-negative disease (rs184090918, OR = 3.70, p = 1.23×10-5; rs76959804, OR = 3.57, p = 1.77×10-5) and on chr16q we identified an association with ER-negative disease (rs34147411, OR = 1.62, p = 8.82×10-6). In the replication study, the chr3 associations were significant and effect sizes were larger (rs184090918, OR: 6.66, 95% CI: 1.43, 31.01; rs76959804, OR: 5.24, 95% CI: 1.70, 16.16). CONCLUSION The two chr3 SNPs are upstream to open chromatin ENSR00000710716, a regulatory feature that is actively regulated in mammary tissues, providing evidence that variants in this chr3 region may have a regulatory role in our target organ. Our study provides support for breast cancer variant discovery using prioritization based on linkage evidence.
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Affiliation(s)
- Heather M Ochs-Balcom
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, 270 Farber Hall, Buffalo, NY 14214, United States
| | - Leah Preus
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, 270 Farber Hall, Buffalo, NY 14214, United States
| | - Zhaohui Du
- Department of Preventive Population and Public Health Sciences, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, 1450 Biggy Street, Los Angeles, CA 90033, United States
- Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, N. Seattle, WA 98109, United States
| | - Robert C Elston
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, United States
| | - Craig C Teerlink
- Department of Internal Medicine, University of Utah School of Medicine, 30 North Mario Capecchi Dr, 3rd Floor North, Salt Lake City, UT 84112, United States
| | - Guochong Jia
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, Nashville, TN 37203, United States
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, Nashville, TN 37203, United States
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, Nashville, TN 37203, United States
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, Nashville, TN 37203, United States
| | - Jie Ping
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, Nashville, TN 37203, United States
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, 707 Light Hall 2215 Garland Avenue, Nashville, TN 37232, United States
| | - Daniel O Stram
- Department of Preventive Population and Public Health Sciences, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, 1450 Biggy Street, Los Angeles, CA 90033, United States
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, Nashville, TN 37203, United States
| | - Maureen Sanderson
- Department of Family and Community Medicine, Meharry Medical College, 1005 Dr. DB Todd Jr, Blvd. Nashville, TN 37208, United States
| | - Guimin Gao
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637, United States
| | - Thomas Ahearn
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, MD 20892, United States
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University, 715 Albany St, Boston, MA 02118, United States
| | - Gary Zirpoli
- Slone Epidemiology Center, Boston University, L-7, 72 East Concord Street, Boston, MA 02118, United States
| | - Melissa A Troester
- Department of Epidemiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 135 Dauer Drive, CB 7435, Chapel Hill, NC 27599, United States
| | - Edward A Ruiz-Narváez
- Department of Nutritional Sciences, University of Michigan School of Public Health, 1860 SPH I, 1415 Washington Heights, Ann Arbor, MI 48109, United States
| | - Stephen A Haddad
- Slone Epidemiology Center, Boston University, L-7, 72 East Concord Street, Boston, MA 02118, United States
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, MD 20892, United States
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh Medical School, 9 Little France Road, Edinburgh, EH16 4UX, United Kingdom
- Cancer Research UK Edinburgh Centre, Crewe Rd S, Edinburgh, EH4 2XR, United Kingdom
| | - Esther M John
- Department of Epidemiology & Population Health, Stanford University School of Medicine, 3145 Porter Dr, Suite E223, MC 5393, Palo Alto, CA 94304, United States
- Department of Medicine (Oncology), Stanford University School of Medicine, 291 Campus Drive Li Ka Shing Building, Stanford, CA 94305, United States
| | - Leslie Bernstein
- Division of Biomarkers of Early Detection and Prevention Department of Population Sciences, Beckman Research Institute of the City of Hope, City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA 91010, United States
| | - Jennifer J Hu
- Sylvester Comprehensive Cancer Center and Department of Public Health Sciences, University of Miami Miller School of Medicine, 1120 NW 14th St, CRB 1511, Miami, FL 33136, United States
| | - Regina G Ziegler
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, MD 20892, United States
| | - Sarah Nyante
- Department of Radiology, School of Medicine, University of North Carolina at Chapel Hill, 130 Mason Farm Rd., Chapel Hill, NC 27599, United States
| | - Elisa V Bandera
- Cancer Epidemiology and Health Outcomes, Rutgers Cancer Institute of New Jersey, 120 Albany Street, Tower 2, 8th Floor, New Brunswick, NJ 08903, United States
| | - Sue A Ingles
- Department of Preventive Population and Public Health Sciences, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, 1450 Biggy Street, Los Angeles, CA 90033, United States
| | - Nicholas Mancuso
- Department of Preventive Population and Public Health Sciences, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, 1450 Biggy Street, Los Angeles, CA 90033, United States
| | - Michael F Press
- Department of Pathology, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, 1441 Eastlake Ave., Los Angeles, CA 90033, United States
| | - Sandra L Deming
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, Nashville, TN 37203, United States
| | - Jorge L Rodriguez-Gil
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, 31 Center Dr, Bethesda, MD 20894, United States
- Medical Scientist Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, 750 Highland Ave., Madison, WI 53705, United States
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, United States
| | - Temidayo O Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Queen Elizabeth II Road, Ibadan, 200285, Nigeria
| | - Oladosu Ojengbede
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, UCH, Queen Elizabeth II Road, Ibadan, 200285, Nigeria
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, 2 Worts Causeway, Cambridge, CB1 8RN, United Kingdom
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, 2 Worts Causeway, Cambridge, CB1 8RN, United Kingdom
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, CB1 8RN, United Kingdom
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, CB1 8RN, United Kingdom
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Iroon Avenue 6, 2371 Ayius Dometios, Nicosia, Cyprus
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, CB1 8RN, United Kingdom
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, PO Box 12233, Research Triangle Park, NC 27709, United States
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, PO Box 12233, Research Triangle Park, NC 27709, United States
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, 2 Worts Causeway, Cambridge, CB1 8RN, United Kingdom
| | - Katie M O’Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, PO Box 12233, Research Triangle Park, NC 27709, United States
| | - Clarice R Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, PO Box 12233, Research Triangle Park, NC 27709, United States
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD 20892, United States
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, Nashville, TN 37203, United States
- International Epidemiology Institute, 1455 Research Boulevard, Rockville, MD 20850, United States
| | - Katherine L Nathanson
- Department of Medicine, Abramson Cancer Center, The Perelman School of Medicine at the University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19140, United States
| | - Anselm Hennis
- Chronic Disease Research Centre and Faculty of Medical Sciences, University of the West Indies, Jemmotts Lane, Avalon, Bridgetown, Barbados
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11794, United States
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, 37 Convent Drive, Bethesda, MD 20892, United States
| | - Lara E Sucheston-Campbell
- College of Pharmacy, The Ohio State University, 217 Lloyd M. Parks Hall, 500 West 12th Ave., Columbus, OH 43210, United States
- College of Veterinary Medicine, The Ohio State University, 1900 Coffey Road, Columbus, OH 43210, United States
| | - Jeannette T Bensen
- Department of Epidemiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 135 Dauer Drive, CB 7435, Chapel Hill, NC 27599, United States
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, MD 20892, United States
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, 170 Rosenau Hall, CB #7400, 135 Dauer Drive, Chapel Hill, NC 27599, United States
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, United States
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, 5841 S Maryland Avenue, Chicago, IL 60637, United States
| | | | - David V Conti
- Department of Preventive Population and Public Health Sciences, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, 1450 Biggy Street, Los Angeles, CA 90033, United States
| | - Julie Palmer
- Slone Epidemiology Center, Boston University, L-7, 72 East Concord Street, Boston, MA 02118, United States
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, MD 20892, United States
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637, United States
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, Nashville, TN 37203, United States
| | - Christopher Haiman
- Department of Preventive Population and Public Health Sciences, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, 1450 Biggy Street, Los Angeles, CA 90033, United States
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Butler EN, Benefield T, Henderson L, Kuzmiak C, Pritchard M, Nyante S. Breast exam use during the protracted COVID-19 pandemic, by age, race, and geography. JNCI Cancer Spectr 2023; 7:7084782. [PMID: 36951539 PMCID: PMC10115465 DOI: 10.1093/jncics/pkad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 03/24/2023] Open
Abstract
In this study we analyzed data collected from the onset of the COVID-19 pandemic through March 31, 2022 to identify temporal shifts in breast exam volume. Screening mammography volume stabilized toward the end of the study period, while diagnostic exam volume varied over time and by age. Older women experienced a decline in diagnostic exam volume between August 2020 and April 2021 that was not observed among women aged 50 years or less (50-69 years, monthly percentage change (MPC): -6.5; and 70+ years, MPC: -15.7). With respect to breast biopsy volume, women younger than 70 years of age had increased exam volume beginning in April 2020 and June 2020, whereas a corresponding increase among older women was delayed until April 2021(70+ years, MPC: 9.3). Findings from our study suggest a temporal shift in the use of breast exams that could result in differential detection of breast cancer by age.
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Affiliation(s)
- Eboneé N Butler
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Thad Benefield
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Louise Henderson
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Cherie Kuzmiak
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Michael Pritchard
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah Nyante
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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3
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Gao G, Zhao F, Ahearn TU, Lunetta KL, Troester MA, Du Z, Ogundiran TO, Ojengbede O, Blot W, Nathanson KL, Domchek SM, Nemesure B, Hennis A, Ambs S, McClellan J, Nie M, Bertrand K, Zirpoli G, Yao S, Olshan AF, Bensen JT, Bandera EV, Nyante S, Conti DV, Press MF, Ingles SA, John EM, Bernstein L, Hu JJ, Deming-Halverson SL, Chanock SJ, Ziegler RG, Rodriguez-Gil JL, Sucheston-Campbell LE, Sandler DP, Taylor JA, Kitahara CM, O’Brien KM, Bolla MK, Dennis J, Dunning AM, Easton DF, Michailidou K, Pharoah PDP, Wang Q, Figueroa J, Biritwum R, Adjei E, Wiafe S, Ambrosone CB, Zheng W, Olopade OI, García-Closas M, Palmer JR, Haiman CA, Huo D. Polygenic risk scores for prediction of breast cancer risk in women of African ancestry: a cross-ancestry approach. Hum Mol Genet 2022; 31:3133-3143. [PMID: 35554533 PMCID: PMC9476624 DOI: 10.1093/hmg/ddac102] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/29/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Polygenic risk scores (PRSs) are useful for predicting breast cancer risk, but the prediction accuracy of existing PRSs in women of African ancestry (AA) remains relatively low. We aim to develop optimal PRSs for the prediction of overall and estrogen receptor (ER) subtype-specific breast cancer risk in AA women. The AA dataset comprised 9235 cases and 10 184 controls from four genome-wide association study (GWAS) consortia and a GWAS study in Ghana. We randomly divided samples into training and validation sets. We built PRSs using individual-level AA data by a forward stepwise logistic regression and then developed joint PRSs that combined (1) the PRSs built in the AA training dataset and (2) a 313-variant PRS previously developed in women of European ancestry. PRSs were evaluated in the AA validation set. For overall breast cancer, the odds ratio per standard deviation of the joint PRS in the validation set was 1.34 [95% confidence interval (CI): 1.27-1.42] with the area under receiver operating characteristic curve (AUC) of 0.581. Compared with women with average risk (40th-60th PRS percentile), women in the top decile of the PRS had a 1.98-fold increased risk (95% CI: 1.63-2.39). For PRSs of ER-positive and ER-negative breast cancer, the AUCs were 0.608 and 0.576, respectively. Compared with existing methods, the proposed joint PRSs can improve prediction of breast cancer risk in AA women.
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Affiliation(s)
- Guimin Gao
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Fangyuan Zhao
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20850, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zhaohui Du
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Temidayo O Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oladosu Ojengbede
- Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Katherine L Nathanson
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Susan M Domchek
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Anselm Hennis
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY 11794, USA
- University of the West Indies, Bridgetown, Bardados
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Julian McClellan
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Mark Nie
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | | | - Gary Zirpoli
- Slone Epidemiology Center, Boston University, Boston, MA 02215, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeannette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Elisa V Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Sarah Nyante
- Department of Radiology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Michael F Press
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Esther M John
- Departments of Epidemiology & Population Health and of Medicine (Oncology) and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Leslie Bernstein
- Biomarkers of Early Detection and Prevention, Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Jennifer J Hu
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Sandra L Deming-Halverson
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20850, USA
| | - Regina G Ziegler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20850, USA
| | - Jorge L Rodriguez-Gil
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, Bethesda, MD 20894, USA
| | - Lara E Sucheston-Campbell
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katie M O’Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Manjeet K Bolla
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Joe Dennis
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Douglas F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia 2371, Cyprus
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Qin Wang
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Jonine Figueroa
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh Medical School, Edinburgh EH16 5TJ, UK
- Cancer Research UK Edinburgh Centre, Edinburgh EH4 2XR, UK
| | | | | | - Seth Wiafe
- School of Public Health, Loma Linda University, Loma Linda, CA 92350, USA
| | | | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics & Global Health, The University of Chicago, Chicago, IL 60637, USA
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20850, USA
| | - Julie R Palmer
- Slone Epidemiology Center, Boston University, Boston, MA 02215, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Dezheng Huo
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
- Center for Clinical Cancer Genetics & Global Health, The University of Chicago, Chicago, IL 60637, USA
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Abubakar M, Mullooly M, Nyante S, Pfeiffer RM, Aiello Bowles EJ, Cora R, Bodelon C, Butler E, Butcher D, Sternberg L, Troester MA, Weinmann S, Sherman M, Glass AG, Berrington de Gonzalez A, Gierach GL. Mammographic Density Decline, Tamoxifen Response, and Prognosis by Molecular Characteristics of Estrogen Receptor-Positive Breast Cancer. JNCI Cancer Spectr 2022; 6:6555998. [PMID: 35583138 PMCID: PMC9070642 DOI: 10.1093/jncics/pkac028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/27/2022] [Accepted: 02/03/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Mammographic breast density (MBD) decline post-tamoxifen initiation is a favorable prognostic factor in estrogen receptor (ER)-positive breast cancer (BC) and has potential utility as a biomarker of tamoxifen response. However, the prognostic value of MBD decline may vary by molecular characteristics among ER-positive patients. METHODS We investigated associations between MBD decline (≥10% vs <10%) and breast cancer-specific mortality (BCSM) among ER-positive breast cancer patients aged 36-87 years at diagnosis treated with tamoxifen at Kaiser Permanente Northwest (1990-2008). Patients who died of BC (case patients; n = 62) were compared with those who did not (control patients; n = 215) overall and by tumor molecular characteristics (immunohistochemistry [IHC]-based subtype [luminal A-like: ER-positive/progesterone receptor [PR]-positive/HER2-negative/low Ki67; luminal B-like: ER-positive and 1 or more of PR-negative, HER2-positive, high Ki67] and modified IHC [mIHC]-based recurrence score of ER/PR/Ki67). Percent MBD was measured in the unaffected breast at baseline mammogram (mean = 6 months before tamoxifen initiation) and follow-up (mean = 12 months post-tamoxifen initiation). Adjusted odds ratios (ORs) and 95% confidence intervals (CIs) were computed from logistic regression models. All statistical tests were 2-sided. RESULTS MBD decline was statistically significantly associated with reduced risk of BCSM overall (OR = 0.38, 95% CI = 0.15 to 0.92). This association was, however, stronger among women with aggressive tumor characteristics including luminal B-like (OR = 0.17, 95% CI = 0.04 to 0.73) vs A-like (OR = 0.74, 95% CI = 0.19 to 2.92); large (OR = 0.26, 95% CI = 0.08 to 0.78) vs small (OR = 0.41, 95% CI = 0.04 to 3.79) tumors; PR-negative (OR = 0.02, 95% CI = 0.001 to 0.37) vs PR-positive (OR = 0.50, 95% CI = 0.18 to 1.40) disease; and high (OR = 0.25, 95% CI = 0.07 to 0.93) vs low (OR = 0.44, 95% CI = 0.10 to 2.09) mIHC3 score. CONCLUSION The findings support MBD decline as a prognostic marker of tamoxifen response among patients with aggressive ER-positive BC phenotypes, for whom understanding treatment effectiveness is critical.
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Affiliation(s)
- Mustapha Abubakar
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA,Correspondence to: Mustapha Abubakar, MD, PhD, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, 9609 Medical Center Drive, Rockville, USA (e-mail: )
| | - Maeve Mullooly
- School of Population Health, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sarah Nyante
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ruth M Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Erin J Aiello Bowles
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
| | - Renata Cora
- Independent Contractor, CT(ASCP), MB(ASCP), Stamford, CT, USA
| | - Clara Bodelon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eboneé Butler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Donna Butcher
- Molecular Histopathology Laboratory, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lawrence Sternberg
- Molecular Histopathology Laboratory, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Melissa A Troester
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sheila Weinmann
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | | | - Andrew G Glass
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | - Amy Berrington de Gonzalez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gretchen L Gierach
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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5
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Du Z, Gao G, Adedokun B, Ahearn T, Lunetta KL, Zirpoli G, Troester MA, Ruiz-Narváez EA, Haddad SA, PalChoudhury P, Figueroa J, John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Mancuso N, Press MF, Deming SL, Rodriguez-Gil JL, Yao S, Ogundiran TO, Ojengbe O, Bolla MK, Dennis J, Dunning AM, Easton DF, Michailidou K, Pharoah PDP, Sandler DP, Taylor JA, Wang Q, Weinberg CR, Kitahara CM, Blot W, Nathanson KL, Hennis A, Nemesure B, Ambs S, Sucheston-Campbell LE, Bensen JT, Chanock SJ, Olshan AF, Ambrosone CB, Olopade OI, Yarney J, Awuah B, Wiafe-Addai B, Conti DV, Palmer JR, Garcia-Closas M, Huo D, Haiman CA. Evaluating Polygenic Risk Scores for Breast Cancer in Women of African Ancestry. J Natl Cancer Inst 2021; 113:1168-1176. [PMID: 33769540 PMCID: PMC8418423 DOI: 10.1093/jnci/djab050] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 02/03/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Polygenic risk scores (PRSs) have been demonstrated to identify women of European, Asian, and Latino ancestry at elevated risk of developing breast cancer (BC). We evaluated the performance of existing PRSs trained in European ancestry populations among women of African ancestry. METHODS We assembled genotype data for women of African ancestry, including 9241 case subjects and 10 193 control subjects. We evaluated associations of 179- and 313-variant PRSs with overall and subtype-specific BC risk. PRS discriminatory accuracy was assessed using area under the receiver operating characteristic curve. We also evaluated a recalibrated PRS, replacing the index variant with variants in each region that better captured risk in women of African ancestry and estimated lifetime absolute risk of BC in African Americans by PRS category. RESULTS For overall BC, the odds ratio per SD of the 313-variant PRS (PRS313) was 1.27 (95% confidence interval [CI] = 1.23 to 1.31), with an area under the receiver operating characteristic curve of 0.571 (95% CI = 0.562 to 0.579). Compared with women with average risk (40th-60th PRS percentile), women in the top decile of PRS313 had a 1.54-fold increased risk (95% CI = 1.38-fold to 1.72-fold). By age 85 years, the absolute risk of overall BC was 19.6% for African American women in the top 1% of PRS313 and 6.7% for those in the lowest 1%. The recalibrated PRS did not improve BC risk prediction. CONCLUSION The PRSs stratify BC risk in women of African ancestry, with attenuated performance compared with that reported in European, Asian, and Latina populations. Future work is needed to improve BC risk stratification for women of African ancestry.
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Affiliation(s)
- Zhaohui Du
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Guimin Gao
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Babatunde Adedokun
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Thomas Ahearn
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Gary Zirpoli
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Melissa A Troester
- Department of Epidemiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Parichoy PalChoudhury
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh Medical School, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Edinburgh, UK
| | - Esther M John
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine (Oncology), Stanford University School of Medicine, Stanford, CA, USA
| | - Leslie Bernstein
- Division of Biomarkers of Early Detection and Prevention Department of Population Sciences, Beckman Research Institute of the City of Hope, City of Hope Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jennifer J Hu
- Department of Public Health Sciences, Sylvester Comprehensive Cancer Center University of Miami Miller School of Medicine, Miami, FL, USA
| | - Regina G Ziegler
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sarah Nyante
- Department of Epidemiology, Gillings School of Global Public Health and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Elisa V Bandera
- Department of Population Science, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Sue A Ingles
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Michael F Press
- Department of Pathology, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Sandra L Deming
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jorge L Rodriguez-Gil
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Medical Scientist Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Temidayo O Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oladosu Ojengbe
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | - Manjeet K Bolla
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Paul D P Pharoah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Qin Wang
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Clarice R Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- International Epidemiology Institute, Rockville, MD, USA
| | - Katherine L Nathanson
- Department of Medicine, Abramson Cancer Center, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Anselm Hennis
- Chronic Disease Research Centre and Faculty of Medical Sciences, University of the West Indies, Bridgetown, Barbados
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, MD, USA
| | - Lara E Sucheston-Campbell
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
- College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Jeannette T Bensen
- Department of Epidemiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Olufunmilayo I Olopade
- Department of Medicine, Center for Clinical Cancer Genetics and Global Health, University of Chicago, Chicago, IL, USA
| | | | | | | | | | | | - Julie R Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA, USA
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6
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Adedokun B, Du Z, Gao G, Ahearn TU, Lunetta KL, Zirpoli G, Figueroa J, John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Deming-Halverson SL, Rodriguez-Gil JL, Yao S, Ogundiran TO, Ojengbede O, Blot W, Troester MA, Nathanson KL, Hennis A, Nemesure B, Ambs S, Fiorica PN, Sucheston-Campbell LE, Bensen JT, Kushi LH, Torres-Mejia G, Hu D, Fejerman L, Bolla MK, Dennis J, Dunning AM, Easton DF, Michailidou K, Pharoah PDP, Wang Q, Sandler DP, Taylor JA, O'Brien KM, Kitahara CM, Falusi AG, Babalola C, Yarney J, Awuah B, Addai-Wiafe B, Chanock SJ, Olshan AF, Ambrosone CB, Conti DV, Ziv E, Olopade OI, Garcia-Closas M, Palmer JR, Haiman CA, Huo D. Cross-ancestry GWAS meta-analysis identifies six breast cancer loci in African and European ancestry women. Nat Commun 2021; 12:4198. [PMID: 34234117 PMCID: PMC8263739 DOI: 10.1038/s41467-021-24327-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 06/02/2021] [Indexed: 02/06/2023] Open
Abstract
Our study describes breast cancer risk loci using a cross-ancestry GWAS approach. We first identify variants that are associated with breast cancer at P < 0.05 from African ancestry GWAS meta-analysis (9241 cases and 10193 controls), then meta-analyze with European ancestry GWAS data (122977 cases and 105974 controls) from the Breast Cancer Association Consortium. The approach identifies four loci for overall breast cancer risk [1p13.3, 5q31.1, 15q24 (two independent signals), and 15q26.3] and two loci for estrogen receptor-negative disease (1q41 and 7q11.23) at genome-wide significance. Four of the index single nucleotide polymorphisms (SNPs) lie within introns of genes (KCNK2, C5orf56, SCAMP2, and SIN3A) and the other index SNPs are located close to GSTM4, AMPD2, CASTOR2, and RP11-168G16.2. Here we present risk loci with consistent direction of associations in African and European descendants. The study suggests that replication across multiple ancestry populations can help improve the understanding of breast cancer genetics and identify causal variants.
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Affiliation(s)
- Babatunde Adedokun
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Zhaohui Du
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Guimin Gao
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Gary Zirpoli
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Jonine Figueroa
- Usher Institute and CRUK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Esther M John
- Departments of Epidemiology & Population Health and of Medicine (Oncology) and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Leslie Bernstein
- Biomarkers of Early Detection and Prevention, Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Jennifer J Hu
- Department of Public Health Sciences, University of Miami, Miami, FL, USA
| | - Regina G Ziegler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Sarah Nyante
- Department of Radiology, University of North Carolina, Chapel Hill, NC, USA
| | - Elisa V Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Sue A Ingles
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michael F Press
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sandra L Deming-Halverson
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Jorge L Rodriguez-Gil
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Temidayo O Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oladosu Ojengbede
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Katherine L Nathanson
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anselm Hennis
- University of the West Indies, Bridgetown, Barbados
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, MD, USA
| | - Peter N Fiorica
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Lara E Sucheston-Campbell
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Jeannette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Gabriela Torres-Mejia
- Center for Population Health Research, Instituto Nacional de Salud Publica, Cuernavaca, Mexico
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Laura Fejerman
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Katie M O'Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Adeyinka G Falusi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Chinedum Babalola
- Department of Pharmaceutical Chemistry, University of Ibadan, Ibadan, Oyo, Nigeria
| | | | | | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - David V Conti
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Elad Ziv
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | - Julie R Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Christopher A Haiman
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Dezheng Huo
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA.
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.
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7
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Alagoz O, Lowry KP, Kurian AW, Mandelblatt JS, Ergun MA, Huang H, Lee SJ, Schecter C, Tosteson AN, Miglioretti DL, Trentham-Dietz A, Nyante S, Kerlikowske K, Sprague BL, Stout NK. Impact of disruptions in breast cancer control due to the COVID-19 pandemic on breast cancer mortality in the United States: Estimates from collaborative simulation modeling. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.6562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
6562 Background: The COVID-19 pandemic has disrupted breast cancer control through short-term declines in screening, delays in diagnosis and reduced/delayed treatments. We projected the impact of COVID-19 on future breast cancer mortality.Methods: Three established Cancer Intervention and Surveillance Modeling Network (CISNET) models projected the impact of pandemic-related care disruptions on breast cancer mortality between 2020 and 2030 vs. pre-pandemic care patterns. Based on Breast Cancer Surveillance Consortium data, we modeled reductions in mammography screening utilization, delays in symptomatic cancer diagnosis, and reduced use of chemotherapy for women with early-stage disease for the first six months of the pandemic with return to pre-pandemic patterns after that time. Sensitivity analyses were performed to determine the effect of key model parameters, including the duration of the pandemic impact. Results: By 2030, the models project 1,297 (model range: 1,054-1,900) cumulative excess deaths related to reduced screening; 1,325 (range: 266-2,628) deaths from delayed diagnosis of symptomatic women, and 207 (range: 146-301) deaths from reduced chemotherapy use for early-stage cancer. Overall, the models predict 2,487 (range 1,713-4,875) excess deaths, representing a 0.56% (range: 0.36%-0.99%) cumulative increase over deaths that would be expected by 2030 in the absence of the pandemic’s disruptions. Sensitivity analyses indicated that the impact on mortality would approximately double if the disruptions lasted for a 12-month period. Conclusions: The impact of the initial pandemic-related disruptions in breast cancer care will have a small long-term cumulative impact on breast cancer mortality. The impact of the initial pandemic-related disruptions on breast cancer mortality will largely be mitigated by the rapid return to usual care. As the pandemic continues it will be important to monitor trends in care and reassess the mortality impact.[Table: see text]
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Affiliation(s)
| | | | | | | | | | - Hui Huang
- Dana-Farber Cancer Institute, Boston, MA
| | - Sandra J. Lee
- Dana-Farber Cancer Institute/Harvard Medical School, Boston, MA
| | - Clyde Schecter
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY
| | | | | | | | - Sarah Nyante
- University of North Carolina-Chapel Hill, Chapel Hill, NC
| | | | | | - Natasha K. Stout
- Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA
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8
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Adedokun B, Du Z, Gao G, Ahearn T, Lunetta KL, Zirpoli G, Figueroa J, John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Deming SL, Rodriguez-Gil JL, Yao S, Ogundiran TO, Ojengbede O, Blot W, Troester M, Nathanson KL, Hennis A, Nemesure B, Ambs S, Sucheston-Campbell LE, Bensen JT, Chanock SJ, Olshan AF, Ambrosone CB, Conti DV, Olopade OI, Garcia-Closas M, Palmer JR, Haiman CA, Huo D. Abstract 4613: Cross-ancestry genome-wide association study identifies six new loci for breast cancer in women of African and european ancestry. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-4613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Over 180 genetic variants have been identified as risk loci for breast cancer. However, most loci were discovered using European ancestry populations. As some common susceptibility loci are shared across populations, we aim to discover new risk loci for breast cancer using a cross-ancestry genome-wide association study (GWAS) approach.
Methods: Data from five GWAS studies in women of African ancestry with a combined sample size of 9241 cases and 10192 controls were used to generate pooled breast cancer risk estimates in a fixed effect meta-analysis, and this served as the discovery dataset. Summary statistics from the GWAS conducted in European ancestry populations (Breast Cancer Association Consortium, 122977 cases and 105974 controls) served as the validation dataset. The variants that were associated with breast cancer risk at P < 0.01 in the GWAS of African ancestry were meta-analyzed with the GWAS in European ancestry. A locus was considered novel if the lead index variant was genome-wide significant (5 × 10−8) in the cross-ancestry meta-analysis and >500kb away from known breast cancer risk loci. Conditional on the lead index variants, we searched for additional signals in each locus using multivariable logistic regression. Analyses were done separately for ER-positive, ER-negative and overall breast cancer risk.
Results: We discovered four novel loci for overall breast cancer risk (1p13.3, 5q31.1, 15q24, and 15q26.3) and two novel loci for ER-negative breast cancer (1q41 and 7q11.23) at the genome-wide significance level of P < 5 × 10−8. Three index single nucleotide polymorphism (SNPs) lie within introns of genes (KCNK2, C5orf56, and SIN3A) and the other index SNPs are located in intergenic regions (close to GSTM4 and AMPD2, CASTOR2, and the antisense DNA RP11-168G16.2). The direction of the associations was consistent between the GWASs of African and European descendants. At the 15q24 locus, we found an additional SNP (in the intron of the SCAMP2 gene) to be independently associated with overall breast cancer risk.
Conclusions: We have identified six new risk loci that may contribute to better prediction of breast cancer risk in African ancestry populations and provide new insights into mechanisms of breast cancer carcinogenesis. Replication of these loci in multiple populations and functional studies can help to identify causal variants.
Citation Format: Babatunde Adedokun, Zhaohui Du, Guimin Gao, Thomas Ahearn, Kathryn L. Lunetta, Gary Zirpoli, Jonine Figueroa, Esther M. John, Leslie Bernstein, Wei Zheng, Jennifer J. Hu, Regina G. Ziegler, Sarah Nyante, Elisa V. Bandera, Sue A. Ingles, Michael F. Press, Sandra L. Deming, Jorge L. Rodriguez-Gil, Song Yao, Temidayo O. Ogundiran, Oladosu Ojengbede, William Blot, Melissa Troester, Katherine L. Nathanson, Anselm Hennis, Barbara Nemesure, Stefan Ambs, Lara E. Sucheston-Campbell, Jeannette T. Bensen, Stephen J. Chanock, Andrew F. Olshan, Christine B. Ambrosone, David V. Conti, Olufunmilayo I. Olopade, Montserrat Garcia-Closas, Julie R. Palmer, Christopher A. Haiman, Dezheng Huo. Cross-ancestry genome-wide association study identifies six new loci for breast cancer in women of African and european ancestry [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4613.
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Affiliation(s)
| | - Zhaohui Du
- 2University of Southern California, Los Angeles, CA
| | | | | | | | | | | | | | | | - Wei Zheng
- 8Vanderbilt University Medical Center, Nashville, TN
| | - Jennifer J. Hu
- 9University of Miami Miller School of Medicine, Miami, FL
| | | | - Sarah Nyante
- 10University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | | | | | | | - Song Yao
- 13Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | | | - William Blot
- 8Vanderbilt University Medical Center, Nashville, TN
| | | | | | - Anselm Hennis
- 16University of the West Indies, Bridgetown, Barbados
| | | | | | | | | | | | - Andrew F. Olshan
- 20University of North Carolina School of Public Health, Chapel Hill, NC
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9
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Du Z, Gao G, Adedokun B, Ahearn T, Lunetta KL, Zirpoli G, Troester M, Ruiz-Narváez EA, Haddad S, Figueroa J, John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Deming SL, Rodriguez-Gil JL, Yao S, Ogundiran TO, Ojengbede OA, Blot W, Nathanson KL, Hennis A, Nemesure B, Ambs S, Sucheston-Campbell LE, Bensen JT, Chanock SJ, Olshan AF, Ambrosone CB, Conti DV, Olopade OI, Palmer JR, Garcia-Closas M, Huo D, Haiman CA. Abstract 2320: Evaluating a polygenic risk score for breast cancer in women of African ancestry. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-2320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: A polygenic risk score (PRS) for breast cancer including 313 common variants developed by the Breast Cancer Association Consortium (BCAC) has been demonstrated to identify women who are at high risk of developing breast cancer [odds ratio (OR 95%CI) = 1.61 (1.57-1.65) per SD] in women of European ancestry. In the present study, we examined the performance of the 313-variant PRS and a PRS including 179 variants reaching genome-wide significance in previous genome-wide association studies (GWAS), in women of African ancestry.
Methods: We assembled genotype data for women of African ancestry from 28 breast cancer studies, including a total of 9,241 cases and 10,193 controls. We constructed the 179-variant and 313-variant PRSs with relative risk weights for each variant estimated in women of European ancestry in BCAC. The associations between the two PRSs and overall, ER+ and ER- breast cancer risk were estimated using logistic regression adjusting for age, study site and principal components. Discriminatory accuracy of the PRSs was evaluated using the receiver operating characteristic curve (AUROC). We then recalibrated the 179-variant PRS by replacing index variants with variants in each region that better captured risk in women of African ancestry and used relative risk weights estimated in women of African ancestry. We also assessed PRS performance by age (<55 versus ≥ 55 years).
Results: Both the 179 and 313- variant PRSs were significantly associated with overall, ER+ and ER- breast cancer risk, with odds ratios (OR) per standard deviation of 1.21~1.37 and AUROCs ranging from 0.57 to 0.59. The 179-variant PRS outperformed in ER- cancer [1.31(1.24,1.37) per SD] while the 313-SNP PRS was better for overall [1.27(1.23,1.31) per SD] and ER+ cancer [1.37(1.32,1.43) per SD]. For overall breast cancer, compared to women with average risk (40th-60th PRS percentiles), women in the top decile of PRS had a 1.54 (95% CI: 1.38, 1.72)-fold increased risk. The performance of the recalibrated 179-variant PRS was not improved (average AUROC=0.56). The PRS ORs did not differ significantly across age strata (P-value for age interaction = 0.63).
Conclusion: Our study shows that both 179 and 313 variant PRS stratify breast cancer risk in women of African ancestry, with attenuated performance compared to that reported in European and in Latina populations. Future work is needed to improve breast cancer risk stratification for women of African ancestry.
Citation Format: Zhaohui Du, Guimin Gao, Babatunde Adedokun, Thomas Ahearn, Kathryn L. Lunetta, Gary Zirpoli, Melissa Troester, Edward A. Ruiz-Narváez, Stephen Haddad, Jonine Figueroa, Esther M. John, Leslie Bernstein, Wei Zheng, Jennifer J. Hu, Regina G. Ziegler, Sarah Nyante, Elisa V. Bandera, Sue A. Ingles, Michael F. Press, Sandra L. Deming, Jorge L. Rodriguez-Gil, Song Yao, Temidayo O. Ogundiran, Oladosu A. Ojengbede, William Blot, Katherine L. Nathanson, Anselm Hennis, Barbara Nemesure, Stefan Ambs, Lara E. Sucheston-Campbell, Jeannette T. Bensen, Stephen J. Chanock, Andrew F. Olshan, Christine B. Ambrosone, David V. Conti, Olufunmilayo I. Olopade, Julie R. Palmer, Montserrat Garcia-Closas, Dezheng Huo, Christopher A. Haiman. Evaluating a polygenic risk score for breast cancer in women of African ancestry [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2320.
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Affiliation(s)
- Zhaohui Du
- 1University of Southern California, Los Angeles, CA
| | | | | | | | | | | | | | | | | | | | | | | | - Wei Zheng
- 10Vanderbilt University, Nashville, TN
| | | | | | - Sarah Nyante
- 5University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | | | | | | | - Song Yao
- 14Roswell Park Cancer Institute, Buffalo, NY
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10
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Huo D, Feng Y, Haddad S, Zheng Y, Yao S, Han YJ, Ogundiran TO, Adebamowo C, Ojengbede O, Falusi AG, Zheng W, Blot W, Cai Q, Signorello L, John EM, Bernstein L, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Deming SL, Rodriguez-Gil JL, Nathanson KL, Domchek SM, Rebbeck TR, Ruiz-Narváez EA, Sucheston-Campbell LE, Bensen JT, Simon MS, Hennis A, Nemesure B, Leske MC, Ambs S, Chen LS, Qian F, Gamazon ER, Lunetta KL, Cox NJ, Chanock SJ, Kolonel LN, Olshan AF, Ambrosone CB, Olopade OI, Palmer JR, Haiman CA. Genome-wide association studies in women of African ancestry identified 3q26.21 as a novel susceptibility locus for oestrogen receptor negative breast cancer. Hum Mol Genet 2018; 25:4835-4846. [PMID: 28171663 DOI: 10.1093/hmg/ddw305] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 07/21/2016] [Accepted: 08/26/2016] [Indexed: 12/20/2022] Open
Abstract
Multiple breast cancer loci have been identified in previous genome-wide association studies, but they were mainly conducted in populations of European ancestry. Women of African ancestry are more likely to have young-onset and oestrogen receptor (ER) negative breast cancer for reasons that are unknown and understudied. To identify genetic risk factors for breast cancer in women of African descent, we conducted a meta-analysis of two genome-wide association studies of breast cancer; one study consists of 1,657 cases and 2,029 controls genotyped with Illumina’s HumanOmni2.5 BeadChip and the other study included 3,016 cases and 2,745 controls genotyped using Illumina Human1M-Duo BeadChip. The top 18,376 single nucleotide polymorphisms (SNP) from the meta-analysis were replicated in the third study that consists of 1,984 African Americans cases and 2,939 controls. We found that SNP rs13074711, 26.5 Kb upstream of TNFSF10 at 3q26.21, was significantly associated with risk of oestrogen receptor (ER)-negative breast cancer (odds ratio [OR]=1.29, 95% CI: 1.18-1.40; P = 1.8 × 10 − 8). Functional annotations suggest that the TNFSF10 gene may be involved in breast cancer aetiology, but further functional experiments are needed. In addition, we confirmed SNP rs10069690 was the best indicator for ER-negative breast cancer at 5p15.33 (OR = 1.30; P = 2.4 × 10 − 10) and identified rs12998806 as the best indicator for ER-positive breast cancer at 2q35 (OR = 1.34; P = 2.2 × 10 − 8) for women of African ancestry. These findings demonstrated additional susceptibility alleles for breast cancer can be revealed in diverse populations and have important public health implications in building race/ethnicity-specific risk prediction model for breast cancer.
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Affiliation(s)
- Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Ye Feng
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Stephen Haddad
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Song Yao
- Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Yoo-Jeong Han
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Temidayo O Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Clement Adebamowo
- Department of Epidemiology & Preventive Medicine, University of Maryland, Baltimore, MD, USA
| | - Oladosu Ojengbede
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeyinka G Falusi
- Institute for Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Lisa Signorello
- Cancer Prevention Fellowship Program, National Cancer Institute, Bethesda, MD, USA
| | - Esther M John
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA.,Cancer Prevention Fellowship Program, National Cancer Institute, Bethesda, MD, USA
| | - Leslie Bernstein
- Division of Cancer Etiology, Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jennifer J Hu
- Sylvester Comprehensive Cancer Center and Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Regina G Ziegler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MA, USA
| | - Sarah Nyante
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | | | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Michael F Press
- Department of Pathology, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Sandra L Deming
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Jorge L Rodriguez-Gil
- Sylvester Comprehensive Cancer Center and Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Susan M Domchek
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy R Rebbeck
- Dana Farber Cancer Institute & Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Jeannette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Michael S Simon
- Karmanos Cancer Institute, Department of Oncology, Wayne State University, Detroit, MI, USA
| | - Anselm Hennis
- Division of Cancer Etiology, Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA.,Sylvester Comprehensive Cancer Center and Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Barbara Nemesure
- Department of Preventive Medicine, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - M Cristina Leske
- Department of Preventive Medicine, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, MD, USA
| | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Frank Qian
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Eric R Gamazon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MA, USA.,Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MA, USA
| | - Laurence N Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | | | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Julie R Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
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11
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Feng Y, Rhie SK, Huo D, Ruiz-Narvaez EA, Haddad SA, Ambrosone CB, John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Deming SL, Rodriguez-Gil JL, Zheng Y, Yao S, Han YJ, Ogundiran TO, Rebbeck TR, Adebamowo C, Ojengbede O, Falusi AG, Hennis A, Nemesure B, Ambs S, Blot W, Cai Q, Signorello L, Nathanson KL, Lunetta KL, Sucheston-Campbell LE, Bensen JT, Chanock SJ, Marchand LL, Olshan AF, Kolonel LN, Conti DV, Coetzee GA, Stram DO, Olopade OI, Palmer JR, Haiman CA. Characterizing Genetic Susceptibility to Breast Cancer in Women of African Ancestry. Cancer Epidemiol Biomarkers Prev 2017; 26:1016-1026. [PMID: 28377418 DOI: 10.1158/1055-9965.epi-16-0567] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/07/2016] [Accepted: 03/15/2017] [Indexed: 01/01/2023] Open
Abstract
Background: Genome-wide association studies have identified approximately 100 common genetic variants associated with breast cancer risk, the majority of which were discovered in women of European ancestry. Because of different patterns of linkage disequilibrium, many of these genetic markers may not represent signals in populations of African ancestry.Methods: We tested 74 breast cancer risk variants and conducted fine-mapping of these susceptibility regions in 6,522 breast cancer cases and 7,643 controls of African ancestry from three genetic consortia (AABC, AMBER, and ROOT).Results: Fifty-four of the 74 variants (73%) were found to have ORs that were directionally consistent with those previously reported, of which 12 were nominally statistically significant (P < 0.05). Through fine-mapping, in six regions (3p24, 12p11, 14q13, 16q12/FTO, 16q23, 19p13), we observed seven markers that better represent the underlying risk variant for overall breast cancer or breast cancer subtypes, whereas in another two regions (11q13, 16q12/TOX3), we identified suggestive evidence of signals that are independent of the reported index variant. Overlapping chromatin features and regulatory elements suggest that many of the risk alleles lie in regions with biological functionality.Conclusions: Through fine-mapping of known susceptibility regions, we have revealed alleles that better characterize breast cancer risk in women of African ancestry.Impact: The risk alleles identified represent genetic markers for modeling and stratifying breast cancer risk in women of African ancestry. Cancer Epidemiol Biomarkers Prev; 26(7); 1016-26. ©2017 AACR.
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Affiliation(s)
- Ye Feng
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California.
| | - Suhn Kyong Rhie
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois
| | | | - Stephen A Haddad
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York
| | - Esther M John
- Cancer Prevention Institute of California, Fremont, California.,Department of Health Research and Policy (Epidemiology) and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Leslie Bernstein
- Division of Cancer Etiology, Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jennifer J Hu
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida
| | - Regina G Ziegler
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Sarah Nyante
- Department of Epidemiology, Gillings School of Global Public Health and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Elisa V Bandera
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Michael F Press
- Department of Pathology, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Sandra L Deming
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jorge L Rodriguez-Gil
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida
| | - Yonglan Zheng
- Department of Medicine, University of Chicago, Chicago, Illinois
| | - Song Yao
- Roswell Park Cancer Institute, Buffalo, New York
| | - Yoo-Jeong Han
- Department of Medicine, University of Chicago, Chicago, Illinois
| | - Temidayo O Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Timothy R Rebbeck
- Dana Farber Cancer Institute & Harvard T. H. Chan School of Public Health, Boston, Maryland
| | - Clement Adebamowo
- Department of Epidemiology & Preventive Medicine, University of Maryland, Baltimore, Maryland
| | - Oladosu Ojengbede
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeyinka G Falusi
- Institute for Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Anselm Hennis
- Chronic Disease Research Centre, Tropical Medicine Research Institute, University of the West Indies, Bridgetown, Barbados.,Department of Preventive Medicine, State University of New York at Stony Brook, Stony Brook, New York
| | - Barbara Nemesure
- Department of Preventive Medicine, State University of New York at Stony Brook, Stony Brook, New York
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, Maryland
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Lisa Signorello
- Cancer Prevention Fellowship Program, National Cancer Institute, Bethesda, Maryland
| | | | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | | | - Jeannette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Stephen J Chanock
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Laurence N Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Gerhard A Coetzee
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Daniel O Stram
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | | | - Julie R Palmer
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California.
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12
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Qian F, Feng Y, Zheng Y, Ogundiran TO, Ojengbede O, Zheng W, Blot W, Ambrosone CB, John EM, Bernstein L, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Nathanson KL, Hennis A, Nemesure B, Ambs S, Kolonel LN, Olopade OI, Haiman CA, Huo D. Genetic variants in microRNA and microRNA biogenesis pathway genes and breast cancer risk among women of African ancestry. Hum Genet 2016; 135:1145-59. [PMID: 27380242 DOI: 10.1007/s00439-016-1707-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/25/2016] [Indexed: 10/21/2022]
Abstract
MicroRNAs (miRNA) regulate breast biology by binding to specific RNA sequences, leading to RNA degradation and inhibition of translation of their target genes. While germline genetic variations may disrupt some of these interactions between miRNAs and their targets, studies assessing the relationship between genetic variations in the miRNA network and breast cancer risk are still limited, particularly among women of African ancestry. We systematically put together a list of 822 and 10,468 genetic variants among primary miRNA sequences and 38 genes in the miRNA biogenesis pathway, respectively; and examined their association with breast cancer risk in the ROOT consortium which includes women of African ancestry. Findings were replicated in an independent consortium. Logistic regression was used to estimate the odds ratio (OR) and 95 % confidence intervals (CI). For overall breast cancer risk, three single-nucleotide polymorphisms (SNPs) in miRNA biogenesis genes DROSHA rs78393591 (OR = 0.69, 95 % CI: 0.55-0.88, P = 0.003), ESR1 rs523736 (OR = 0.88, 95 % CI: 0.82-0.95, P = 3.99 × 10(-4)), and ZCCHC11 rs114101502 (OR = 1.33, 95 % CI: 1.11-1.59, P = 0.002), and one SNP in primary miRNA sequence (rs116159732 in miR-6826, OR = 0.74, 95 % CI: 0.63-0.89, P = 0.001) were found to have significant associations in both discovery and validation phases. In a subgroup analysis, two SNPs were associated with risk of estrogen receptor (ER)-negative breast cancer, and three SNPs were associated with risk of ER-positive breast cancer. Several variants in miRNA and miRNA biogenesis pathway genes were associated with breast cancer risk. Risk associations varied by ER status, suggesting potential new mechanisms in etiology.
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Affiliation(s)
- Frank Qian
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Ye Feng
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Yonglan Zheng
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Temidayo O Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oladosu Ojengbede
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | | | - Esther M John
- Cancer Prevention Institute of California, Fremont, CA, USA.,Department of Health Research and Policy (Epidemiology) and Stanford Cancer Institute, Stanford University School of Medicine Stanford, Stanford, CA, USA
| | - Leslie Bernstein
- Division of Cancer Etiology, Department of Population Science, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Jennifer J Hu
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Regina G Ziegler
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, DC, USA
| | - Sarah Nyante
- Department of Epidemiology, Gillings School of Global Public Health and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Elisa V Bandera
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Michael F Press
- Department of Pathology, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | | | - Anselm Hennis
- Chronic Disease Research Centre and Tropical Medicine Research Institute, University of the West Indies, Bridgetown, Barbados
| | - Barbara Nemesure
- Department of Preventive Medicine, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, MD, USA
| | - Laurence N Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | | | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., MC 2007, Chicago, IL, 60637, USA.
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13
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Mullooly M, Yang HP, Falk RT, Nyante S, Cora R, Pfeiffer RM, Radisky DC, Visscher DW, Hartmann LC, Degnim AC, Stanczyk FZ, Figueroa JF, Garcia-Closas M, Lissowska J, Troester MT, Brinton LA, Sherman ME, Gierach GL. Abstract 2767: Investigation of the relationship between crown-like structures and adipose tissue hormone levels among postmenopausal women with breast cancer. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-2767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Increased levels of circulating estrogens are associated with elevated risks of postmenopausal breast cancer. Previously, we showed that levels of sex steroid hormones in breast adipose tissue are positively correlated with circulating hormones. Further evaluation of hormone levels in breast tissues may help to explain the relationship between estrogens and breast cancer risk. Specifically, data suggest that focal breast lesions consisting of macrophages encircling dying adipocytes, referred to as “crown-like structures (CLS)”, are associated with increased aromatase activity, which could increase conversion of androgens to estrogens locally in the breast. Therefore, we assessed whether the presence of CLS affects the correlations between blood and breast adipose tissue hormone levels. Methods: Participants included 84 postmenopausal women with invasive breast cancer in the Polish Breast Cancer Study, a population based case-control study conducted from 2000 to 2003. We previously reported sex steroid hormone levels in cancer-free breast adipose tissue removed as part of breast excisions performed for cancer. Here, using immunohistochemical stains, we evaluated the number of CD68 positive macrophages and the presence of full CLS (i.e., complete adipocyte encirclement) in benign breast tissue sections prepared from surgical pathology specimens containing breast cancer. The relationship between the number of CD68 positive macrophages per unit area of fat and hormone levels was examined using Spearman rank correlations (rs). We assessed potential effect modification of the association between blood and tissue hormone levels by presence or absence of CLS by including an interaction term in linear regression models. Results: The number of CD68 positive macrophages per unit area of fat was not significantly correlated with levels of estrone, estradiol, androstenedione or testosterone measured in blood (rs = 0.001, -0.04, -0.07, and -0.09, respectively; p>0.05) or breast adipose tissue (rs = -0.15, 0.06, -0.06, and -0.08, respectively; p>0.05). Correlations between serum and adipose tissue hormones did not statistically significantly differ between women with CLS (n = 30) compared to those without CLS (n = 54). CLS were found more frequently in breast adipose tissue from overweight (i.e., women with a body mass index (BMI) between 25 and 29.9) (43%) and obese women (BMI >30) (30%) versus normal weight women, with (BMI between 18.5 and 24.9), (27%); (p = 0.04, χ2 test). The number of CD68 positive macrophages per unit area of fat was not significantly related to BMI (p = 0.31). Conclusion: Among postmenopausal women with invasive breast cancer, the presence of CLS was more common among overweight and obese women, but CLS did not influence the correlation between circulating and breast adipose tissue sex steroid hormone levels.
Citation Format: Maeve Mullooly, Hannah P. Yang, Roni T. Falk, Sarah Nyante, Renata Cora, Ruth M. Pfeiffer, Derek C. Radisky, Daniel W. Visscher, Lynn C. Hartmann, Amy C. Degnim, Frank Z. Stanczyk, Jonine F. Figueroa, Montserrat Garcia-Closas, Jolanta Lissowska, Melissa T. Troester, Louise A. Brinton, Mark E. Sherman, Gretchen L. Gierach. Investigation of the relationship between crown-like structures and adipose tissue hormone levels among postmenopausal women with breast cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2767. doi:10.1158/1538-7445.AM2015-2767
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Affiliation(s)
- Maeve Mullooly
- 1Hormonal and Reproductive Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute and Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
| | - Hannah P. Yang
- 2Hormonal and Reproductive Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Roni T. Falk
- 2Hormonal and Reproductive Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Sarah Nyante
- 2Hormonal and Reproductive Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Renata Cora
- 3Independent contractor, CT(ASCP), MB(ASCP), Stamford, CT
| | - Ruth M. Pfeiffer
- 4Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | | | | | | | | | - Frank Z. Stanczyk
- 6Department of Obstetrics and Gynecology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jonine F. Figueroa
- 2Hormonal and Reproductive Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | | | - Jolanta Lissowska
- 8Department of Cancer Epidemiology and Prevention, Cancer Center and M. Sklodowska-Curie Institute of Oncology, Warsaw, Poland
| | - Melissa T. Troester
- 9Department of Epidemiology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Louise A. Brinton
- 2Hormonal and Reproductive Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Mark E. Sherman
- 10Breast and Gynecologic Cancer Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
| | - Gretchen L. Gierach
- 2Hormonal and Reproductive Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
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14
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Chen F, He J, Zhang J, Chen GK, Thomas V, Ambrosone CB, Bandera EV, Berndt SI, Bernstein L, Blot WJ, Cai Q, Carpten J, Casey G, Chanock SJ, Cheng I, Chu L, Deming SL, Driver WR, Goodman P, Hayes RB, Hennis AJM, Hsing AW, Hu JJ, Ingles SA, John EM, Kittles RA, Kolb S, Leske MC, Millikan RC, Monroe KR, Murphy A, Nemesure B, Neslund-Dudas C, Nyante S, Ostrander EA, Press MF, Rodriguez-Gil JL, Rybicki BA, Schumacher F, Stanford JL, Signorello LB, Strom SS, Stevens V, Van Den Berg D, Wang Z, Witte JS, Wu SY, Yamamura Y, Zheng W, Ziegler RG, Stram AH, Kolonel LN, Marchand LL, Henderson BE, Haiman CA, Stram DO. Methodological Considerations in Estimation of Phenotype Heritability Using Genome-Wide SNP Data, Illustrated by an Analysis of the Heritability of Height in a Large Sample of African Ancestry Adults. PLoS One 2015; 10:e0131106. [PMID: 26125186 PMCID: PMC4488332 DOI: 10.1371/journal.pone.0131106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 05/28/2015] [Indexed: 01/02/2023] Open
Abstract
Height has an extremely polygenic pattern of inheritance. Genome-wide association studies (GWAS) have revealed hundreds of common variants that are associated with human height at genome-wide levels of significance. However, only a small fraction of phenotypic variation can be explained by the aggregate of these common variants. In a large study of African-American men and women (n = 14,419), we genotyped and analyzed 966,578 autosomal SNPs across the entire genome using a linear mixed model variance components approach implemented in the program GCTA (Yang et al Nat Genet 2010), and estimated an additive heritability of 44.7% (se: 3.7%) for this phenotype in a sample of evidently unrelated individuals. While this estimated value is similar to that given by Yang et al in their analyses, we remain concerned about two related issues: (1) whether in the complete absence of hidden relatedness, variance components methods have adequate power to estimate heritability when a very large number of SNPs are used in the analysis; and (2) whether estimation of heritability may be biased, in real studies, by low levels of residual hidden relatedness. We addressed the first question in a semi-analytic fashion by directly simulating the distribution of the score statistic for a test of zero heritability with and without low levels of relatedness. The second question was addressed by a very careful comparison of the behavior of estimated heritability for both observed (self-reported) height and simulated phenotypes compared to imputation R2 as a function of the number of SNPs used in the analysis. These simulations help to address the important question about whether today's GWAS SNPs will remain useful for imputing causal variants that are discovered using very large sample sizes in future studies of height, or whether the causal variants themselves will need to be genotyped de novo in order to build a prediction model that ultimately captures a large fraction of the variability of height, and by implication other complex phenotypes. Our overall conclusions are that when study sizes are quite large (5,000 or so) the additive heritability estimate for height is not apparently biased upwards using the linear mixed model; however there is evidence in our simulation that a very large number of causal variants (many thousands) each with very small effect on phenotypic variance will need to be discovered to fill the gap between the heritability explained by known versus unknown causal variants. We conclude that today's GWAS data will remain useful in the future for causal variant prediction, but that finding the causal variants that need to be predicted may be extremely laborious.
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Affiliation(s)
- Fang Chen
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America
| | - Jing He
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America
| | - Jianqi Zhang
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America
| | - Gary K. Chen
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America
| | - Venetta Thomas
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, FL, United States of America
| | - Christine B. Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, United States of America
| | - Elisa V. Bandera
- The Cancer Institute of New Jersey, New Brunswick, NJ, United States of America
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Leslie Bernstein
- Division of Cancer Etiology, Department of Population Science, Beckman Research Institute, City of Hope, CA, United States of America
| | - William J. Blot
- International Epidemiology Institute, Rockville, MD, United States of America
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University and the Vanderbilt-Ingram Cancer Center, Nashville, TN, United States of America
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University and the Vanderbilt-Ingram Cancer Center, Nashville, TN, United States of America
| | - John Carpten
- The Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Graham Casey
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Iona Cheng
- Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, HI, United States of America
| | - Lisa Chu
- Cancer Prevention Institute of California, Fremont, CA, United States of America
| | - Sandra L. Deming
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University and the Vanderbilt-Ingram Cancer Center, Nashville, TN, United States of America
| | - W. Ryan Driver
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, United States of America
| | - Phyllis Goodman
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Richard B. Hayes
- Division of Epidemiology, Department of Environmental Medicine, New York University Langone Medical Center, New York, NY, United States of America
| | - Anselm J. M. Hennis
- Chronic Disease Research Centre and Faculty of Medical Sciences, University of the West Indies, Bridgetown, Barbados
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, United States of America
| | - Ann W. Hsing
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Jennifer J. Hu
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, FL, United States of America
| | - Sue A. Ingles
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America
| | - Esther M. John
- Cancer Prevention Institute of California, Fremont, CA, United States of America
- Division of Epidemiology, Department of Health Research & Policy, Stanford University School of Medicine and Stanford Cancer Institute, Stanford, CA, United States of America
| | - Rick A. Kittles
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - M. Cristina Leske
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, United States of America
| | - Robert C. Millikan
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States of America
| | - Kristine R. Monroe
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America
| | - Adam Murphy
- Department of Urology, Northwestern University, Chicago, IL, United States of America
| | - Barbara Nemesure
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, United States of America
| | - Christine Neslund-Dudas
- Department of Biostatistics and Research Epidemiology, Henry Ford Hospital, Detroit, MI, United States of America
| | - Sarah Nyante
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Elaine A Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Michael F. Press
- Department of Pathology, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America
| | - Jorge L. Rodriguez-Gil
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, FL, United States of America
| | - Ben A. Rybicki
- Department of Biostatistics and Research Epidemiology, Henry Ford Hospital, Detroit, MI, United States of America
| | - Fredrick Schumacher
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America
| | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Lisa B. Signorello
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, United States of America
| | - Sara S. Strom
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States of America
| | - Victoria Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, United States of America
| | - David Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - John S. Witte
- Institute for Human Genetics, Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, United States of America
| | - Suh-Yuh Wu
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, United States of America
| | - Yuko Yamamura
- Institute for Human Genetics, Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, United States of America
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University and the Vanderbilt-Ingram Cancer Center, Nashville, TN, United States of America
| | - Regina G. Ziegler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Alexander H. Stram
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America
| | - Laurence N. Kolonel
- Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, HI, United States of America
| | - Loïc Le Marchand
- Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, HI, United States of America
| | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America
| | - Daniel O. Stram
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America
- * E-mail:
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15
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Feng Y, Stram DO, Rhie SK, Millikan RC, Ambrosone CB, John EM, Bernstein L, Zheng W, Olshan AF, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Deming SL, Rodriguez-Gil JL, Palmer JR, Olopade OI, Huo D, Adebamowo CA, Ogundiran T, Chen GK, Stram A, Park K, Rand KA, Chanock SJ, Le Marchand L, Kolonel LN, Conti DV, Easton D, Henderson BE, Haiman CA. A comprehensive examination of breast cancer risk loci in African American women. Hum Mol Genet 2014; 23:5518-26. [PMID: 24852375 PMCID: PMC4168823 DOI: 10.1093/hmg/ddu252] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 05/04/2014] [Accepted: 05/19/2014] [Indexed: 12/18/2022] Open
Abstract
Genome-wide association studies have identified 73 breast cancer risk variants mainly in European populations. Given considerable differences in linkage disequilibrium structure between populations of European and African ancestry, the known risk variants may not be informative for risk in African ancestry populations. In a previous fine-mapping investigation of 19 breast cancer loci, we were able to identify SNPs in four regions that better captured risk associations in African American women. In this study of breast cancer in African American women (3016 cases, 2745 controls), we tested an additional 54 novel breast cancer risk variants. Thirty-eight variants (70%) were found to have an association with breast cancer in the same direction as previously reported, with eight (15%) replicating at P < 0.05. Through fine-mapping, in three regions (1q32, 3p24, 10q25), we identified variants that better captured associations with overall breast cancer or estrogen receptor positive disease. We also observed suggestive associations with variants (at P < 5 × 10(-6)) in three separate regions (6q25, 14q13, 22q12) that may represent novel risk variants. Directional consistency of association observed for ∼65-70% of currently known genetic variants for breast cancer in women of African ancestry implies a shared functional common variant at most loci. To validate and enhance the spectrum of alleles that define associations at the known breast cancer risk loci, as well as genome-wide, will require even larger collaborative efforts in women of African ancestry.
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Affiliation(s)
- Ye Feng
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center and
| | - Daniel O Stram
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center and
| | - Suhn Kyong Rhie
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center and
| | - Robert C Millikan
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Esther M John
- Cancer Prevention Institute of California, Fremont, CA, USA Division of Epidemiology, Department of Health Research & Policy, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Leslie Bernstein
- Division of Cancer Etiology, Department of Population Science, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Jennifer J Hu
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Regina G Ziegler
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics and
| | - Sarah Nyante
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Elisa V Bandera
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center and
| | - Michael F Press
- Department of Pathology, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Sandra L Deming
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jorge L Rodriguez-Gil
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Julie R Palmer
- Slone Epidemiology Center at Boston University, Boston, MA, USA
| | | | - Dezheng Huo
- Department of Health Studies, University of Chicago, Chicago, IL, USA
| | - Clement A Adebamowo
- Department of Epidemiology & Preventive Medicine, University of Maryland, Baltimore, MD, USA
| | - Temidayo Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Gary K Chen
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center and
| | - Alex Stram
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center and
| | - Karen Park
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center and
| | - Kristin A Rand
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center and
| | - Stephen J Chanock
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics and
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Laurence N Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center and
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center and
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center and
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16
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Bhatia G, Tandon A, Patterson N, Aldrich M, Ambrosone C, Amos C, Bandera E, Berndt S, Bernstein L, Blot W, Bock C, Caporaso N, Casey G, Deming S, Diver W, Gapstur S, Gillanders E, Harris C, Henderson B, Ingles S, Isaacs W, De Jager P, John E, Kittles R, Larkin E, McNeill L, Millikan R, Murphy A, Neslund-Dudas C, Nyante S, Press M, Rodriguez-Gil J, Rybicki B, Schwartz A, Signorello L, Spitz M, Strom S, Tucker M, Wiencke J, Witte J, Wu X, Yamamura Y, Zanetti K, Zheng W, Ziegler R, Chanock S, Haiman C, Reich D, Price A. Genome-wide scan of 29,141 African Americans finds no evidence of directional selection since admixture. Am J Hum Genet 2014; 95:437-44. [PMID: 25242497 DOI: 10.1016/j.ajhg.2014.08.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 08/22/2014] [Indexed: 10/24/2022] Open
Abstract
The extent of recent selection in admixed populations is currently an unresolved question. We scanned the genomes of 29,141 African Americans and failed to find any genome-wide-significant deviations in local ancestry, indicating no evidence of selection influencing ancestry after admixture. A recent analysis of data from 1,890 African Americans reported that there was evidence of selection in African Americans after their ancestors left Africa, both before and after admixture. Selection after admixture was reported on the basis of deviations in local ancestry, and selection before admixture was reported on the basis of allele-frequency differences between African Americans and African populations. The local-ancestry deviations reported by the previous study did not replicate in our very large sample, and we show that such deviations were expected purely by chance, given the number of hypotheses tested. We further show that the previous study's conclusion of selection in African Americans before admixture is also subject to doubt. This is because the FST statistics they used were inflated and because true signals of unusual allele-frequency differences between African Americans and African populations would be best explained by selection that occurred in Africa prior to migration to the Americas.
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Feng Y, Chen GK, Stram DO, Millikan RC, Ambrosone CB, John EM, Bernstein L, Zheng W, Olshan AF, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Deming SL, Rodriguez-Gil JL, Palmer JR, Olopade OI, Huo D, Adebamowo CA, Ogundiran T, Stram A, Park K, Rand KA, Chanock SJ, Marchand LL, Kolonel LN, Conti DV, Easton D, Henderson BE, Haiman CA. Abstract 943: A comprehensive examination of breast cancer risk loci in African American women. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Genome-wide association studies have identified 73 breast cancer risk variants mainly in European populations. Given considerable differences in linkage disequilibrium structure between populations of European and African ancestry, the known risk variants may not be informative for risk in African populations. In a previous fine-mapping investigation of 19 breast cancer loci, we were able to identify SNPs in 4 regions that better defined risk associations in African American women. In this study of breast cancer in African American women (3,016 cases, 2,745 controls), we tested an additional 54 novel breast cancer risk variants. Thirty-eight variants (70%) showed an association with breast cancer in the same direction as previously reported, with eight (15%) replicating at p<0.05. Through fine-mapping, in three regions (1q32, 3p24, 10q25) we identified variants that better captured associations with overall breast cancer or estrogen receptor positive disease. We also observed suggestive associations with variants (at p<5×10-6) in three separate regions (6q25, 14q13, 22q12) that may represent novel risk variants, with one variant at the PAX9 locus replicating in an independent sample (1,657 cases and 2,028 controls of African ancestry; rs17104923, p=0.057). Directional consistency of association observed for ∼65-70% of currently known genetic variants for breast cancer in women of African ancestry implies a shared functional common variant at most loci. To validate and enhance the spectrum of alleles that define associations at the known breast cancer risk loci, as well as genome-wide, will require even larger collaborative efforts in women of African ancestry.
Citation Format: Ye Feng, Gary K. Chen, Daniel O. Stram, Robert C. Millikan, Christine B. Ambrosone, Esther M. John, Leslie Bernstein, Wei Zheng, Andrew F. Olshan, Jennifer J. Hu, Regina G. Ziegler, Sarah Nyante, Elisa V. Bandera, Sue A. Ingles, Michael F. Press, Sandra L. Deming, Jorge L. Rodriguez-Gil, Julie R. Palmer, Olufunmilayo I. Olopade, Dezheng Huo, Clement A. Adebamowo, Temidayo Ogundiran, Alex Stram, Karen Park, Kristin A. Rand, Stephen J. Chanock, Loic Le Marchand, Laurence N. Kolonel, David V. Conti, Douglas Easton, Brian E. Henderson, Christopher A. Haiman. A comprehensive examination of breast cancer risk loci in African American women. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 943. doi:10.1158/1538-7445.AM2014-943
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Affiliation(s)
- Ye Feng
- 1University of Southern California, Los Angeles, CA
| | - Gary K. Chen
- 1University of Southern California, Los Angeles, CA
| | | | | | | | | | | | - Wei Zheng
- 6Vanderbilt University School of Medicine, Nashville, TN
| | | | - Jennifer J. Hu
- 7University of Miami Miller School of Medicine, Miami, FL
| | | | | | | | | | | | | | | | - Julie R. Palmer
- 10Slone Epidemiology Center at Boston University, Boston, MA
| | | | | | | | | | - Alex Stram
- 1University of Southern California, Los Angeles, CA
| | - Karen Park
- 1University of Southern California, Los Angeles, CA
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18
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Liu CT, Monda KL, Taylor KC, Lange L, Demerath EW, Palmas W, Wojczynski MK, Ellis JC, Vitolins MZ, Liu S, Papanicolaou GJ, Irvin MR, Xue L, Griffin PJ, Nalls MA, Adeyemo A, Liu J, Li G, Ruiz-Narvaez EA, Chen WM, Chen F, Henderson BE, Millikan RC, Ambrosone CB, Strom SS, Guo X, Andrews JS, Sun YV, Mosley TH, Yanek LR, Shriner D, Haritunians T, Rotter JI, Speliotes EK, Smith M, Rosenberg L, Mychaleckyj J, Nayak U, Spruill I, Garvey WT, Pettaway C, Nyante S, Bandera EV, Britton AF, Zonderman AB, Rasmussen-Torvik LJ, Chen YDI, Ding J, Lohman K, Kritchevsky SB, Zhao W, Peyser PA, Kardia SLR, Kabagambe E, Broeckel U, Chen G, Zhou J, Wassertheil-Smoller S, Neuhouser ML, Rampersaud E, Psaty B, Kooperberg C, Manson JE, Kuller LH, Ochs-Balcom HM, Johnson KC, Sucheston L, Ordovas JM, Palmer JR, Haiman CA, McKnight B, Howard BV, Becker DM, Bielak LF, Liu Y, Allison MA, Grant SFA, Burke GL, Patel SR, Schreiner PJ, Borecki IB, Evans MK, Taylor H, Sale MM, Howard V, Carlson CS, Rotimi CN, Cushman M, Harris TB, Reiner AP, Cupples LA, North KE, Fox CS. Genome-wide association of body fat distribution in African ancestry populations suggests new loci. PLoS Genet 2013; 9:e1003681. [PMID: 23966867 PMCID: PMC3744443 DOI: 10.1371/journal.pgen.1003681] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 06/13/2013] [Indexed: 01/18/2023] Open
Abstract
Central obesity, measured by waist circumference (WC) or waist-hip ratio (WHR), is a marker of body fat distribution. Although obesity disproportionately affects minority populations, few studies have conducted genome-wide association study (GWAS) of fat distribution among those of predominantly African ancestry (AA). We performed GWAS of WC and WHR, adjusted and unadjusted for BMI, in up to 33,591 and 27,350 AA individuals, respectively. We identified loci associated with fat distribution in AA individuals using meta-analyses of GWA results for WC and WHR (stage 1). Overall, 25 SNPs with single genomic control (GC)-corrected p-values<5.0 × 10(-6) were followed-up (stage 2) in AA with WC and with WHR. Additionally, we interrogated genomic regions of previously identified European ancestry (EA) WHR loci among AA. In joint analysis of association results including both Stage 1 and 2 cohorts, 2 SNPs demonstrated association, rs2075064 at LHX2, p = 2.24×10(-8) for WC-adjusted-for-BMI, and rs6931262 at RREB1, p = 2.48×10(-8) for WHR-adjusted-for-BMI. However, neither signal was genome-wide significant after double GC-correction (LHX2: p = 6.5 × 10(-8); RREB1: p = 5.7 × 10(-8)). Six of fourteen previously reported loci for waist in EA populations were significant (p<0.05 divided by the number of independent SNPs within the region) in AA studied here (TBX15-WARS2, GRB14, ADAMTS9, LY86, RSPO3, ITPR2-SSPN). Further, we observed associations with metabolic traits: rs13389219 at GRB14 associated with HDL-cholesterol, triglycerides, and fasting insulin, and rs13060013 at ADAMTS9 with HDL-cholesterol and fasting insulin. Finally, we observed nominal evidence for sexual dimorphism, with stronger results in AA women at the GRB14 locus (p for interaction = 0.02). In conclusion, we identified two suggestive loci associated with fat distribution in AA populations in addition to confirming 6 loci previously identified in populations of EA. These findings reinforce the concept that there are fat distribution loci that are independent of generalized adiposity.
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Affiliation(s)
- Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Keri L. Monda
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kira C. Taylor
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Epidemiology and Population Health, University of Louisville, Louisville, Kentucky, United States of America
| | - Leslie Lange
- Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Ellen W. Demerath
- University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Walter Palmas
- Department of Medicine, Columbia University, New York, New York, United States of America
| | - Mary K. Wojczynski
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jaclyn C. Ellis
- Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Mara Z. Vitolins
- Department of Epidemiology & Prevention, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
| | - Simin Liu
- Departments of Epidemiology, Medicine, and Obstetrics and Gynecology and Center for Metabolic Disease Prevention, Los Angeles, California, United States of America
| | - George J. Papanicolaou
- Division of Cardiovascular Sciences, Prevention and Population Sciences Program, National Heart, Lung, & Blood Institute, Bethesda, Maryland, United States of America
| | - Marguerite R. Irvin
- Department of Epidemiology, UAB, Birmingham, Alabama, United States of America
| | - Luting Xue
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Paula J. Griffin
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Michael A. Nalls
- Laboratory of Neurogenetics, National Institute of Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Jiankang Liu
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Guo Li
- University of Washington, Seattle, Washington, United States of America
| | - Edward A. Ruiz-Narvaez
- Slone Epidemiology Center, Boston University, Boston, Massachusetts, United States of America
| | - Wei-Min Chen
- Center for Public Health and Genomics and Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Fang Chen
- Center for Public Health and Genomics and Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Robert C. Millikan
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, UNC at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Christine B. Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Sara S. Strom
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Xiuqing Guo
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Jeanette S. Andrews
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Yan V. Sun
- Department of Epidemiolgy, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Thomas H. Mosley
- Division of Geriatrics, Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Lisa R. Yanek
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Talin Haritunians
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Jerome I. Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | | | - Megan Smith
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Lynn Rosenberg
- Slone Epidemiology Center, Boston University, Boston, Massachusetts, United States of America
| | - Josyf Mychaleckyj
- Center for Public Health and Genomics and Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Uma Nayak
- Center for Public Health and Genomics and Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Ida Spruill
- Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - W. Timothy Garvey
- Department of Epidemiology, UAB School of Public Health, Birmingham, Alabama, United States of America
| | - Curtis Pettaway
- Department of Urology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Sarah Nyante
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, UNC at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Elisa V. Bandera
- The Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America
| | - Angela F. Britton
- Laboratory of Neurogenetics, National Institute of Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alan B. Zonderman
- Laboratory of Personality and Cognition, National Institute on Aging, National Institutes of Health, NIH Biomedical Center, Baltimore, Maryland, United States of America
| | - Laura J. Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Yii-Der Ida Chen
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Jingzhong Ding
- Department of Internal Medicine/Geriatrics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Kurt Lohman
- Department of Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Stephen B. Kritchevsky
- Department of Internal Medicine/Geriatrics, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Wei Zhao
- Department of Epidemiolgy, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Patricia A. Peyser
- Department of Epidemiolgy, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sharon L. R. Kardia
- Department of Epidemiolgy, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Edmond Kabagambe
- Department of Epidemiology, UAB, Birmingham, Alabama, United States of America
| | - Ulrich Broeckel
- Department of Pediatrics, Medicine and Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Jie Zhou
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Sylvia Wassertheil-Smoller
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Marian L. Neuhouser
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Evadnie Rampersaud
- Miami Institute for Human Genomics, Miami, Florida, United States of America
- John T. McDonald Department of Human Genetics, University of Miami, Miami, Florida, United States of America
| | - Bruce Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services and Group Health Research Institute, Group Health Cooperative, Seattle, Washington, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - JoAnn E. Manson
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lewis H. Kuller
- Department of Epidemiology, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Heather M. Ochs-Balcom
- Department of Social and Preventive Medicine, University at Buffalo, Buffalo, New York, United States of America
| | - Karen C. Johnson
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Lara Sucheston
- Department of Biostatistics, University of Buffalo School of Public Health and Health Professions, New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York, United States of America
| | - Jose M. Ordovas
- Tufts University, Boston, Massachusetts, United States of America
| | - Julie R. Palmer
- Slone Epidemiology Center, Boston University, Boston, Massachusetts, United States of America
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Barbara V. Howard
- MedStar Health Research Institute and Georgetown University, Hyattsville, Maryland, United States of America
| | - Diane M. Becker
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Lawrence F. Bielak
- Department of Epidemiolgy, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Matthew A. Allison
- University of California at San Diego Department of Preventive Medicine, La Jolla, California, United States of America
| | - Struan F. A. Grant
- Division of Human Genetics, Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, United States of America
| | - Gregory L. Burke
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Sanjay R. Patel
- Division of Sleep Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Pamela J. Schreiner
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ingrid B. Borecki
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michele K. Evans
- Health Disparities Research Section, Clinical Research Branch, National Institute on Aging, National Institutes of Health, NIH Biomedical Center, Baltimore, Maryland, United States of America
| | - Herman Taylor
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Michele M. Sale
- Center for Public Genomics, Department of Biochemistry and Molecular Genetics and Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Virginia Howard
- Department of Epidemiology, UAB School of Public Health, Birmingham, Alabama, United States of America
| | - Christopher S. Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Mary Cushman
- Department of Medicine, University of Vermont, Colchester, Vermont, United States of America
| | - Tamara B. Harris
- Laboratory of Epidemiology, Demography, and Biometry, NIA, Bethesda, Maryland, United States of America
| | - Alexander P. Reiner
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
- NHLBI's Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Kari E. North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (KEN); (CSF)
| | - Caroline S. Fox
- NHLBI's Framingham Heart Study, Framingham, Massachusetts, United States of America
- NHLBI's Center for Population Studies, Framingham, Massachusetts, United States of America
- Division of Endocrinology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (KEN); (CSF)
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19
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Demerath EW, Liu CT, Franceschini N, Chen G, Palmer JR, Smith EN, Chen CTL, Ambrosone CB, Arnold AM, Bandera EV, Berenson GS, Bernstein L, Britton A, Cappola AR, Carlson CS, Chanock SJ, Chen W, Chen Z, Deming SL, Elks CE, Evans MK, Gajdos Z, Henderson BE, Hu JJ, Ingles S, John EM, Kerr KF, Kolonel LN, Le Marchand L, Lu X, Millikan RC, Musani SK, Nock NL, North K, Nyante S, Press MF, Rodriquez-Gil JL, Ruiz-Narvaez EA, Schork NJ, Srinivasan SR, Woods NF, Zheng W, Ziegler RG, Zonderman A, Heiss G, Gwen Windham B, Wellons M, Murray SS, Nalls M, Pastinen T, Rajkovic A, Hirschhorn J, Adrienne Cupples L, Kooperberg C, Murabito JM, Haiman CA. Genome-wide association study of age at menarche in African-American women. Hum Mol Genet 2013; 22:3329-46. [PMID: 23599027 DOI: 10.1093/hmg/ddt181] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
African-American (AA) women have earlier menarche on average than women of European ancestry (EA), and earlier menarche is a risk factor for obesity and type 2 diabetes among other chronic diseases. Identification of common genetic variants associated with age at menarche has a potential value in pointing to the genetic pathways underlying chronic disease risk, yet comprehensive genome-wide studies of age at menarche are lacking for AA women. In this study, we tested the genome-wide association of self-reported age at menarche with common single-nucleotide polymorphisms (SNPs) in a total of 18 089 AA women in 15 studies using an additive genetic linear regression model, adjusting for year of birth and population stratification, followed by inverse-variance weighted meta-analysis (Stage 1). Top meta-analysis results were then tested in an independent sample of 2850 women (Stage 2). First, while no SNP passed the pre-specified P < 5 × 10(-8) threshold for significance in Stage 1, suggestive associations were found for variants near FLRT2 and PIK3R1, and conditional analysis identified two independent SNPs (rs339978 and rs980000) in or near RORA, strengthening the support for this suggestive locus identified in EA women. Secondly, an investigation of SNPs in 42 previously identified menarche loci in EA women demonstrated that 25 (60%) of them contained variants significantly associated with menarche in AA women. The findings provide the first evidence of cross-ethnic generalization of menarche loci identified to date, and suggest a number of novel biological links to menarche timing in AA women.
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Affiliation(s)
- Ellen W Demerath
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA.
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20
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Garcia-Closas M, Couch FJ, Lindstrom S, Michailidou K, Schmidt MK, Brook MN, orr N, Rhie SK, Riboli E, Feigelson HS, Le Marchand L, Buring JE, Eccles D, Miron P, Fasching PA, Brauch H, Chang-Claude J, Carpenter J, Godwin AK, Nevanlinna H, Giles GG, Cox A, Hopper JL, Bolla MK, Wang Q, Dennis J, Dicks E, Howat WJ, Schoof N, Bojesen SE, Lambrechts D, Broeks A, Andrulis IL, Guénel P, Burwinkel B, Sawyer EJ, Hollestelle A, Fletcher O, Winqvist R, Brenner H, Mannermaa A, Hamann U, Meindl A, Lindblom A, Zheng W, Devillee P, Goldberg MS, Lubinski J, Kristensen V, Swerdlow A, Anton-Culver H, Dörk T, Muir K, Matsuo K, Wu AH, Radice P, Teo SH, Shu XO, Blot W, Kang D, Hartman M, Sangrajrang S, Shen CY, Southey MC, Park DJ, Hammet F, Stone J, Veer LJV, Rutgers EJ, Lophatananon A, Stewart-Brown S, Siriwanarangsan P, Peto J, Schrauder MG, Ekici AB, Beckmann MW, Silva IDS, Johnson N, Warren H, Tomlinson I, Kerin MJ, Miller N, Marme F, Schneeweiss A, Sohn C, Truong T, Laurent-Puig P, Kerbrat P, Nordestgaard BG, Nielsen SF, Flyger H, Milne RL, Perez JIA, Menéndez P, Müller H, Arndt V, Stegmaier C, Lichtner P, Lochmann M, Justenhoven C, Ko YD, Muranen TA, Aittomäki K, Blomqvist C, Greco D, Heikkinen T, Ito H, Iwata H, Yatabe Y, Antonenkova NN, Margolin S, Kataja V, Kosma VM, Hartikainen JM, Balleine R, Tseng CC, Van Den Berg D, Stram DO, Neven P, Dieudonné AS, Leunen K, Rudolph A, Nickels S, Flesch-Janys D, Peterlongo P, Peissel B, Bernard L, Olson JE, Wang X, Stevens K, Severi G, Baglietto L, Mclean C, Coetzee GA, Feng Y, Henderson BE, Schumacher F, Bogdanova NV, Labrèche F, Dumont M, Yip CH, Taib NAM, Cheng CY, Shrubsole M, Long J, Pylkäs K, Jukkola-Vuorinen A, Kauppila S, knight JA, Glendon G, Mulligan AM, Tollenaar RAEM, Seynaeve CM, Kriege M, Hooning MJ, Van den Ouweland AMW, Van Deurzen CHM, Lu W, Gao YT, Cai H, Balasubramanian SP, Cross SS, Reed MWR, Signorello L, Cai Q, Shah M, Miao H, Chan CW, Chia KS, Jakubowska A, Jaworska K, Durda K, Hsiung CN, Wu PE, Yu JC, Ashworth A, Jones M, Tessier DC, González-Neira A, Pita G, Alonso MR, Vincent D, Bacot F, Ambrosone CB, Bandera EV, John EM, Chen GK, Hu JJ, Rodriguez-gil JL, Bernstein L, Press MF, Ziegler RG, Millikan RM, Deming-Halverson SL, Nyante S, Ingles SA, Waisfisz Q, Tsimiklis H, Makalic E, Schmidt D, Bui M, Gibson L, Müller-Myhsok B, Schmutzler RK, Hein R, Dahmen N, Beckmann L, Aaltonen K, Czene K, Irwanto A, Liu J, Turnbull C, Rahman N, Meijers-Heijboer H, Uitterlinden AG, Rivadeneira F, Olswold C, Slager S, Pilarski R, Ademuyiwa F, Konstantopoulou I, Martin NG, Montgomery GW, Slamon DJ, Rauh C, Lux MP, Jud SM, Bruning T, Weaver J, Sharma P, Pathak H, Tapper W, Gerty S, Durcan L, Trichopoulos D, Tumino R, Peeters PH, Kaaks R, Campa D, Canzian F, Weiderpass E, Johansson M, Khaw KT, Travis R, Clavel-Chapelon F, Kolonel LN, Chen C, Beck A, Hankinson SE, Berg CD, Hoover RN, Lissowska J, Figueroa JD, Chasman DI, Gaudet MM, Diver WR, Willett WC, Hunter DJ, Simard J, Benitez J, Dunning AM, Sherman ME, Chenevix-Trench G, Chanock SJ, Hall P, Pharoah PDP, Vachon C, Easton DF, Haiman CA, Kraft P. Genome-wide association studies identify four ER negative-specific breast cancer risk loci. Nat Genet 2013; 45:392-8, 398e1-2. [PMID: 23535733 PMCID: PMC3771695 DOI: 10.1038/ng.2561] [Citation(s) in RCA: 323] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 01/29/2013] [Indexed: 12/14/2022]
Abstract
Estrogen receptor (ER)-negative tumors represent 20-30% of all breast cancers, with a higher proportion occurring in younger women and women of African ancestry. The etiology and clinical behavior of ER-negative tumors are different from those of tumors expressing ER (ER positive), including differences in genetic predisposition. To identify susceptibility loci specific to ER-negative disease, we combined in a meta-analysis 3 genome-wide association studies of 4,193 ER-negative breast cancer cases and 35,194 controls with a series of 40 follow-up studies (6,514 cases and 41,455 controls), genotyped using a custom Illumina array, iCOGS, developed by the Collaborative Oncological Gene-environment Study (COGS). SNPs at four loci, 1q32.1 (MDM4, P = 2.1 × 10(-12) and LGR6, P = 1.4 × 10(-8)), 2p24.1 (P = 4.6 × 10(-8)) and 16q12.2 (FTO, P = 4.0 × 10(-8)), were associated with ER-negative but not ER-positive breast cancer (P > 0.05). These findings provide further evidence for distinct etiological pathways associated with invasive ER-positive and ER-negative breast cancers.
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Affiliation(s)
- Montserrat Garcia-Closas
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Fergus J Couch
- Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Sara Lindstrom
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Marjanka K Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Mark N Brook
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Nick orr
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Suhn Kyong Rhie
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Elio Riboli
- School of Public Health, Imperial College, London, UK
| | | | - Loic Le Marchand
- Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, Hawaii, USA
| | - Julie E Buring
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Diana Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Penelope Miron
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen, Erlangen, Germany
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jane Carpenter
- Australian Breast Cancer Tissue Bank, University of Sydney at the Westmead Millennium Institute, Westmead, New South Wales, Australia
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Graham G Giles
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Victoria, Australia
- School of Population Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Angela Cox
- Cancer Research UK/Yorkshire Cancer Research Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield, UK
| | - John L Hopper
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Ed Dicks
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Will J Howat
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Nils Schoof
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Stig E Bojesen
- Copenhagen General Population Study, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Diether Lambrechts
- Vesalius Research Center (VRC), VIB, Leuven, Belgium
- Department of Oncology, University of Leuven, Leuven, Belgium
| | - Annegien Broeks
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Irene L Andrulis
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Ontario Cancer Genetics Network, Fred A. Litwin Center for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Pascal Guénel
- University Paris–Sud, Unité Mixte de Recherche Scientifique (UMRS) 1018, Villejuif, France
- INSERM (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), Environmental Epidemiology of Cancer, Villejuif, France
| | - Barbara Burwinkel
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- Molecular Epidemiology Group, DKFZ, Heidelberg, Germany
| | - Elinor J Sawyer
- Division of Cancer Studies, National Institute for Health Research (NIHR) Comprehensive Biomedical Research Centre, Guy’s & St. Thomas’ National Health Service (NHS) Foundation Trust in partnership with King’s College London, London, UK
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus University Medical Center–Daniel Den Hoed Cancer Center, Rotterdam, The Netherlands
| | - Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Genetics, Biocenter Oulu, University of Oulu, Oulu University Hospital, Oulu, Finland
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, DKFZ, Heidelberg, Germany
| | - Arto Mannermaa
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
- Biocenter Kuopio, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, DKFZ, Heidelberg, Germany
| | - Alfons Meindl
- Division for Gynaecological Tumor Genetics, Clinic of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
- Division of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Wei Zheng
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Peter Devillee
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mark S Goldberg
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Division of Clinical Epidemiology, McGill University Health Centre, Royal Victoria Hospital, Montreal, Quebec, Canada
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway
- Faculty of Medicine (Faculty Division Ahus), Universitetet i Oslo, Oslo, Norway
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California–Irvine, Irvine, California, USA
| | - Thilo Dörk
- Department of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Kenneth Muir
- Warwick Medical School, Warwick University, Coventry, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Keitaro Matsuo
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Soo Hwang Teo
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Subang Jaya, University Malaya Cancer Research Institute, University Malaya, Kuala Lumpur, Malaysia
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, University Malaya, Kuala Lumpur, Malaysia
| | - Xiao-Ou Shu
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - William Blot
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- International Epidemiology Institute, Rockville, Maryland, USA
| | - Daehee Kang
- Seoul National University College of Medicine, Seoul, Korea
| | - Mikael Hartman
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | | | - Chen-Yang Shen
- Colleague of Public Health, China Medical University, Taichong, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Melissa C Southey
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel J Park
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Fleur Hammet
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jennifer Stone
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Laura J Van’t Veer
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Emiel J Rutgers
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | | | | | | | - Julian Peto
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Michael G Schrauder
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen, Erlangen, Germany
| | - Isabel dos Santos Silva
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Nichola Johnson
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Helen Warren
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Michael J Kerin
- Department of Surgery, Clinical Science Institute, University Hospital and National University of Ireland, Galway, Ireland
| | - Nicola Miller
- Department of Surgery, Clinical Science Institute, University Hospital and National University of Ireland, Galway, Ireland
| | - Federick Marme
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Andreas Schneeweiss
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Christof Sohn
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Therese Truong
- University Paris–Sud, Unité Mixte de Recherche Scientifique (UMRS) 1018, Villejuif, France
- INSERM (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), Environmental Epidemiology of Cancer, Villejuif, France
| | | | - Pierre Kerbrat
- Centre Eugène Marquis, Department of Medical Oncology, Rennes, France
| | - Børge G Nordestgaard
- Copenhagen General Population Study, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Sune F Nielsen
- Copenhagen General Population Study, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Roger L Milne
- Genetic & Molecular Epidemiology Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | | | - Heiko Müller
- Division of Clinical Epidemiology and Aging Research, DKFZ, Heidelberg, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, DKFZ, Heidelberg, Germany
| | | | - Peter Lichtner
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
| | - Magdalena Lochmann
- Division of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
| | - Christina Justenhoven
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn, Johanniter Krankenhaus, Bonn, Germany
| | | | - Taru A Muranen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Central Hospital, Helsinki, Finland
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Central Hospital, Helsinki, Finland
| | - Dario Greco
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Tuomas Heikkinen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Hidemi Ito
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Hiroji Iwata
- Department of Breast Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Natalia N Antonenkova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Sara Margolin
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Vesa Kataja
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, Kuopio, Finland
- Biocenter Kuopio, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Cancer Center, Kuopio University Hospital, Kuopio, Finland
| | - Veli-Matti Kosma
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
- Biocenter Kuopio, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
| | - Jaana M Hartikainen
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
- Biocenter Kuopio, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
| | - Rosemary Balleine
- Western Sydney Local Health District, Westmead Millennium Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
- Nepean Blue Mountains Local Health District, Westmead Millennium Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | | | - Chiu-Chen Tseng
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - David Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Daniel O Stram
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Patrick Neven
- Multidisciplinary Breast Center, University Hospital Gasthuisberg, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Anne-Sophie Dieudonné
- Multidisciplinary Breast Center, University Hospital Gasthuisberg, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Karin Leunen
- Multidisciplinary Breast Center, University Hospital Gasthuisberg, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Nickels
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Flesch-Janys
- Department of Cancer Epidemiology/Clinical Cancer Registry, University Clinic Hamburg-Eppendorf, Hamburg, Germany
- Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Paolo Peterlongo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS INT, Milan, Italy
| | - Loris Bernard
- Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy
- Cogentech Cancer Genetic Test Laboratory, Milan, Italy
| | - Janet E Olson
- Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Xianshu Wang
- Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Laboratory Medicine and Pathology, Division of Experimental Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Kristen Stevens
- Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Gianluca Severi
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Laura Baglietto
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Catriona Mclean
- Department of Anatomical Pathology, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Gerhard A Coetzee
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Ye Feng
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Fredrick Schumacher
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Natalia V Bogdanova
- Department of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
| | - France Labrèche
- Département de Médecine Sociale et Préventive, Département de Santé Environnementale et Santé au Travail, Université de Montréal, Montreal, Quebec, Canada
| | - Martine Dumont
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Quebec City, Quebec, Canada
| | - Cheng Har Yip
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, University Malaya, Kuala Lumpur, Malaysia
| | - Nur Aishah Mohd Taib
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, University Malaya, Kuala Lumpur, Malaysia
| | - Ching-Yu Cheng
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Singapore Eye Research Institute, National University of Singapore, Singapore
| | - Martha Shrubsole
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Jirong Long
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Genetics, Biocenter Oulu, University of Oulu, Oulu University Hospital, Oulu, Finland
| | | | - Saila Kauppila
- Department of Pathology, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Julia A knight
- Ontario Cancer Genetics Network, Fred A. Litwin Center for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Gord Glendon
- Ontario Cancer Genetics Network, Fred A. Litwin Center for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine, Keenan Research Centre of the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Ontario, Canada
| | | | - Caroline M Seynaeve
- Department of Medical Oncology, Erasmus University Medical Center–Daniel Den Hoed Cancer Center, Rotterdam, The Netherlands
| | - Mieke Kriege
- Department of Medical Oncology, Erasmus University Medical Center–Daniel Den Hoed Cancer Center, Rotterdam, The Netherlands
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus University Medical Center–Daniel Den Hoed Cancer Center, Rotterdam, The Netherlands
| | | | | | - Wei Lu
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Hui Cai
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Sabapathy P Balasubramanian
- Cancer Research UK/Yorkshire Cancer Research Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Malcolm W R Reed
- Cancer Research UK/Yorkshire Cancer Research Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Lisa Signorello
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Qiuyin Cai
- Division of Clinical Epidemiology, McGill University Health Centre, Royal Victoria Hospital, Montreal, Quebec, Canada
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Hui Miao
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Ching Wan Chan
- Department of Surgery, National University Health System, Singapore
| | - Kee Seng Chia
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Jaworska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Durda
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Chia-Ni Hsiung
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Pei-Ei Wu
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jyh-Cherng Yu
- Department of Surgery, Tri-Service General Hospital, Taipei, Taiwan
| | - Alan Ashworth
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Michael Jones
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Daniel C Tessier
- McGill University and Génome Québec Innovation Centre, Montreal, Québec, Canada
| | - Anna González-Neira
- Human Genotyping Unit–CEGEN, Human Cancer Genetics Programme, CNIO, Madrid, Spain
| | - Guillermo Pita
- Human Genotyping Unit–CEGEN, Human Cancer Genetics Programme, CNIO, Madrid, Spain
| | - M Rosario Alonso
- Human Genotyping Unit–CEGEN, Human Cancer Genetics Programme, CNIO, Madrid, Spain
| | - Daniel Vincent
- McGill University and Génome Québec Innovation Centre, Montreal, Québec, Canada
| | - Francois Bacot
- McGill University and Génome Québec Innovation Centre, Montreal, Québec, Canada
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Elisa V Bandera
- The Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Esther M John
- Cancer Prevention Institute of California, Fremont, California, USA
- Department of Health Research and Policy, Division of Epidemiology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Gary K Chen
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Jennifer J Hu
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA
- Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Jorge L Rodriguez-gil
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA
- Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Leslie Bernstein
- Division of Cancer Etiology, Department of Population Science, Beckman Research Institute, City of Hope, Duarte, California, USA
| | - Michael F Press
- Department of Pathology, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Regina G Ziegler
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Robert M Millikan
- Department of Epidemiology, Gillings School of Global Public Health, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sandra L Deming-Halverson
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Sarah Nyante
- Department of Epidemiology, Gillings School of Global Public Health, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Quinten Waisfisz
- Section of Oncogenetics, Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Helen Tsimiklis
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Enes Makalic
- School of Population Health, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel Schmidt
- School of Population Health, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Minh Bui
- School of Population Health, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lorna Gibson
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Bertram Müller-Myhsok
- Statistical Genetics Research Group, Max Planck Institute of Psychiatry, Munich, Germany
| | - Rita K Schmutzler
- Centre of Hereditary Breast and Ovarian Cancer, University Hospital, Cologne, Germany
- Centre of Integrated Oncology, University Hospital, Cologne, Germany
| | - Rebecca Hein
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- PMV (Primärmedizinische Versorgung) Research Group, Department of Child and Adolescent Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany
| | - Norbert Dahmen
- Department of Psychiatry, University of Mainz, Mainz, Germany
| | - Lars Beckmann
- Institute for Quality and Efficiency in Health Care (IQWiG), Cologne, Germany
| | - Kirsimari Aaltonen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
- Department of Clinical Genetics, Helsinki University Central Hospital, Helsinki, Finland
- Department of Oncology, Helsinki University Central Hospital, Helsinki, Finland
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Astrid Irwanto
- Human Genetics Division, Genome Institute of Singapore, Singapore
| | - Jianjun Liu
- Human Genetics Division, Genome Institute of Singapore, Singapore
| | - Clare Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | | | - Nazneen Rahman
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Hanne Meijers-Heijboer
- Section of Oncogenetics, Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Andre G Uitterlinden
- Department of Internal Medicine and Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine and Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Curtis Olswold
- Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Susan Slager
- Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Robert Pilarski
- Department of Internal Medicine, James Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, USA
| | | | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, Institute of Radioisotopes and Radiodiagnostic Products (IRRP), National Centre for Scientific Research Demokritos, Aghia Paraskevi Attikis, Athens, Greece
| | - Nicholas G Martin
- QIMR GWAS Collective, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Grant W Montgomery
- QIMR GWAS Collective, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Dennis J Slamon
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Department of Medicine, Division of Hematology and Oncology, University of California, Los Angeles, Los Angeles, California, USA
| | - Claudia Rauh
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen, Erlangen, Germany
| | - Michael P Lux
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen, Erlangen, Germany
| | - Sebastian M Jud
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen, Erlangen, Germany
| | - Thomas Bruning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance (IPA), Bochum, Germany
| | - Joellen Weaver
- Biosample Repository, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Priyanka Sharma
- Division of Hematology and Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Harsh Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Will Tapper
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sue Gerty
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Lorraine Durcan
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Dimitrios Trichopoulos
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
- Bureau of Epidemiologic Research, Academy of Athens, Athens, Greece
- Hellenic Health Foundation, Athens, Greece
| | - Rosario Tumino
- Cancer Registry, Histopathology Unit Civile MPArezzo Hospital, Ragusa, Italy
| | - Petra H Peeters
- Julius Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniele Campa
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Federico Canzian
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elisabete Weiderpass
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Community Medicine, University of Tromsø, Tromsø, Norway
- Cancer Registry of Norway, Oslo, Norway
| | - Mattias Johansson
- Genetic Epidemiology Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge, UK
| | - Ruth Travis
- Cancer Epidemiology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Françoise Clavel-Chapelon
- University Paris–Sud, Unité Mixte de Recherche Scientifique (UMRS) 1018, Villejuif, France
- INSERM (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), Environmental Epidemiology of Cancer, Villejuif, France
| | - Laurence N Kolonel
- Département de Médecine Sociale et Préventive, Département de Santé Environnementale et Santé au Travail, Université de Montréal, Montreal, Quebec, Canada
| | - Constance Chen
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Andy Beck
- Department of Pathology, Beth Israel DeaconessMedical Center, Boston, Massachusetts, USA
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Susan E Hankinson
- Division of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, Massachusetts, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Christine D Berg
- Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, USA
| | - Robert N Hoover
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jonine D Figueroa
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Mia M Gaudet
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Walter C Willett
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
| | - David J Hunter
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Jacques Simard
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Quebec City, Quebec, Canada
| | - Javier Benitez
- Human Genotyping Unit–CEGEN, Human Cancer Genetics Programme, CNIO, Madrid, Spain
- Human Genetics Group, CNIO, Madrid, Spain
- Centro de Investigacion en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Mark E Sherman
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Georgia Chenevix-Trench
- Department of Genetics, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Stephen J Chanock
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Celine Vachon
- Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
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21
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Song C, Chen GK, Millikan RC, Ambrosone CB, John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Deming SL, Rodriguez-Gil JL, Chanock SJ, Wan P, Sheng X, Pooler LC, Van Den Berg DJ, Le Marchand L, Kolonel LN, Henderson BE, Haiman CA, Stram DO. A genome-wide scan for breast cancer risk haplotypes among African American women. PLoS One 2013; 8:e57298. [PMID: 23468962 PMCID: PMC3585353 DOI: 10.1371/journal.pone.0057298] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 01/23/2013] [Indexed: 12/03/2022] Open
Abstract
Genome-wide association studies (GWAS) simultaneously investigating hundreds of thousands of single nucleotide polymorphisms (SNP) have become a powerful tool in the investigation of new disease susceptibility loci. Haplotypes are sometimes thought to be superior to SNPs and are promising in genetic association analyses. The application of genome-wide haplotype analysis, however, is hindered by the complexity of haplotypes themselves and sophistication in computation. We systematically analyzed the haplotype effects for breast cancer risk among 5,761 African American women (3,016 cases and 2,745 controls) using a sliding window approach on the genome-wide scale. Three regions on chromosomes 1, 4 and 18 exhibited moderate haplotype effects. Furthermore, among 21 breast cancer susceptibility loci previously established in European populations, 10p15 and 14q24 are likely to harbor novel haplotype effects. We also proposed a heuristic of determining the significance level and the effective number of independent tests by the permutation analysis on chromosome 22 data. It suggests that the effective number was approximately half of the total (7,794 out of 15,645), thus the half number could serve as a quick reference to evaluating genome-wide significance if a similar sliding window approach of haplotype analysis is adopted in similar populations using similar genotype density.
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Affiliation(s)
- Chi Song
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Gary K. Chen
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Robert C. Millikan
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Christine B. Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Esther M. John
- Cancer Prevention Institute of California, Fremont, California, United States of America
- Stanford University School of Medicine and Stanford Cancer Institute, Stanford, California, United States of America
| | - Leslie Bernstein
- Division of Cancer Etiology, Department of Population Science, Beckman Research Institute, City of Hope, Duarte, California, United States of America
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Jennifer J. Hu
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Regina G. Ziegler
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Sarah Nyante
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Elisa V. Bandera
- The Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America
| | - Sue A. Ingles
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Michael F. Press
- Department of Pathology, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Sandra L. Deming
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Jorge L. Rodriguez-Gil
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Stephen J. Chanock
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Peggy Wan
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Xin Sheng
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Loreall C. Pooler
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - David J. Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
- Epigenome Center, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Laurence N. Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Chris A. Haiman
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Daniel O. Stram
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
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22
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Donninger H, Barnoud T, Nelson N, Kassler S, Clark J, Cummins TD, Powell DW, Nyante S, Millikan RC, Clark GJ. RASSF1A and the rs2073498 Cancer Associated SNP. Front Oncol 2011; 1:54. [PMID: 22649770 PMCID: PMC3355887 DOI: 10.3389/fonc.2011.00054] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 12/06/2011] [Indexed: 12/23/2022] Open
Abstract
RASSF1A is one of the most frequently inactivated tumor suppressors yet identified in human cancer. It is pro-apoptotic and appears to function as a scaffolding protein that interacts with a variety of other tumor suppressors to modulate their function. It can also complex with the Ras oncoprotein and may serve to integrate pro-growth and pro-death signaling pathways. A SNP has been identified that is present in approximately 29% of European populations [rs2073498, A(133)S]. Several studies have now presented evidence that this SNP is associated with an enhanced risk of developing breast cancer. We have used a proteomics based approach to identify multiple differences in the pattern of protein/protein interactions mediated by the wild type compared to the SNP variant protein. We have also identified a significant difference in biological activity between wild type and SNP variant protein. However, we have found only a very modest association of the SNP with breast cancer predisposition.
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Affiliation(s)
- Howard Donninger
- Molecular Targets Program, Department of Medicine, James Graham Brown Cancer Center, University of Louisville Louisville, KY, USA
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23
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N'Diaye A, Chen GK, Palmer CD, Ge B, Tayo B, Mathias RA, Ding J, Nalls MA, Adeyemo A, Adoue V, Ambrosone CB, Atwood L, Bandera EV, Becker LC, Berndt SI, Bernstein L, Blot WJ, Boerwinkle E, Britton A, Casey G, Chanock SJ, Demerath E, Deming SL, Diver WR, Fox C, Harris TB, Hernandez DG, Hu JJ, Ingles SA, John EM, Johnson C, Keating B, Kittles RA, Kolonel LN, Kritchevsky SB, Le Marchand L, Lohman K, Liu J, Millikan RC, Murphy A, Musani S, Neslund-Dudas C, North KE, Nyante S, Ogunniyi A, Ostrander EA, Papanicolaou G, Patel S, Pettaway CA, Press MF, Redline S, Rodriguez-Gil JL, Rotimi C, Rybicki BA, Salako B, Schreiner PJ, Signorello LB, Singleton AB, Stanford JL, Stram AH, Stram DO, Strom SS, Suktitipat B, Thun MJ, Witte JS, Yanek LR, Ziegler RG, Zheng W, Zhu X, Zmuda JM, Zonderman AB, Evans MK, Liu Y, Becker DM, Cooper RS, Pastinen T, Henderson BE, Hirschhorn JN, Lettre G, Haiman CA. Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry. PLoS Genet 2011; 7:e1002298. [PMID: 21998595 PMCID: PMC3188544 DOI: 10.1371/journal.pgen.1002298] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 07/26/2011] [Indexed: 11/19/2022] Open
Abstract
Adult height is a classic polygenic trait of high heritability (h2 ∼0.8). More than 180 single nucleotide polymorphisms (SNPs), identified mostly in populations of European descent, are associated with height. These variants convey modest effects and explain ∼10% of the variance in height. Discovery efforts in other populations, while limited, have revealed loci for height not previously implicated in individuals of European ancestry. Here, we performed a meta-analysis of genome-wide association (GWA) results for adult height in 20,427 individuals of African ancestry with replication in up to 16,436 African Americans. We found two novel height loci (Xp22-rs12393627, P = 3.4×10−12 and 2p14-rs4315565, P = 1.2×10−8). As a group, height associations discovered in European-ancestry samples replicate in individuals of African ancestry (P = 1.7×10−4 for overall replication). Fine-mapping of the European height loci in African-ancestry individuals showed an enrichment of SNPs that are associated with expression of nearby genes when compared to the index European height SNPs (P<0.01). Our results highlight the utility of genetic studies in non-European populations to understand the etiology of complex human diseases and traits. Adult height is an ideal phenotype to improve our understanding of the genetic architecture of complex diseases and traits: it is easily measured and usually available in large cohorts, relatively stable, and mostly influenced by genetics (narrow-sense heritability of height h2∼0.8). Genome-wide association (GWA) studies in individuals of European ancestry have identified >180 single nucleotide polymorphisms (SNPs) associated with height. In the current study, we continued to use height as a model polygenic trait and explored the genetic influence in populations of African ancestry through a meta-analysis of GWA height results from 20,809 individuals of African descent. We identified two novel height loci not previously found in Europeans. We also replicated the European height signals, suggesting that many of the genetic variants that are associated with height are shared between individuals of European and African descent. Finally, in fine-mapping the European height loci in African-ancestry individuals, we found SNPs more likely to be associated with the expression of nearby genes than the SNPs originally found in Europeans. Thus, our results support the utility of performing genetic studies in non-European populations to gain insights into complex human diseases and traits.
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Affiliation(s)
| | - Gary K. Chen
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Cameron D. Palmer
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Divisions of Genetics and Endocrinology and Program in Genomics, Children's Hospital Boston, Boston, Massachusetts, United States of America
| | - Bing Ge
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | - Bamidele Tayo
- Department of Preventive Medicine and Epidemiology, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois, United States of America
| | - Rasika A. Mathias
- Department of Medicine, The Johns Hopkins GeneSTAR Research Program, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jingzhong Ding
- Sticht Center on Aging, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Michael A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Adebowale Adeyemo
- NIH Intramural Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Véronique Adoue
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | - Christine B. Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Larry Atwood
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Elisa V. Bandera
- The Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America
| | - Lewis C. Becker
- Department of Medicine, The Johns Hopkins GeneSTAR Research Program, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Leslie Bernstein
- Division of Cancer Etiology, Department of Population Science, Beckman Research Institute, City of Hope, Duarte, California, United States of America
| | - William J. Blot
- International Epidemiology Institute, Rockville, Maryland, United States of America
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt–Ingram Cancer Center, Nashville, Tennessee, United States of America
| | - Eric Boerwinkle
- Human Genetics Center and Institute of Molecular Medicine and Division of Epidemiology, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Angela Britton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Graham Casey
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ellen Demerath
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, Minnesota, United States of America
| | - Sandra L. Deming
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt–Ingram Cancer Center, Nashville, Tennessee, United States of America
| | - W. Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, United States of America
| | - Caroline Fox
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Tamara B. Harris
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Dena G. Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jennifer J. Hu
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Sue A. Ingles
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Esther M. John
- Cancer Prevention Institute of California, Fremont, California, United States of America
- School of Medicine and Stanford Cancer Center, Stanford University, Stanford, California, United States of America
| | - Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Brendan Keating
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Rick A. Kittles
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Laurence N. Kolonel
- Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Stephen B. Kritchevsky
- Sticht Center on Aging, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Loic Le Marchand
- Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Kurt Lohman
- Sticht Center on Aging, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Jiankang Liu
- University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Robert C. Millikan
- Department of Epidemiology, Gillings School of Global Public Health and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Adam Murphy
- Department of Urology, Northwestern University, Chicago, Illinois, United States of America
| | - Solomon Musani
- Jackson Heart Study, Department of Medicine, Division of Cardiovascular Disease, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Christine Neslund-Dudas
- Department of Biostatistics and Research Epidemiology, Henry Ford Hospital, Detroit, Michigan, United States of America
| | - Kari E. North
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Sarah Nyante
- Department of Epidemiology, Gillings School of Global Public Health and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | | | - Elaine A. Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - George Papanicolaou
- National Heart, Lung, and Blood Institute (NHLBI), Division of Cardiovascular Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sanjay Patel
- Division of Sleep Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Curtis A. Pettaway
- Department of Urology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Michael F. Press
- Department of Pathology, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Susan Redline
- Division of Sleep Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Jorge L. Rodriguez-Gil
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Charles Rotimi
- NIH Intramural Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Benjamin A. Rybicki
- Department of Biostatistics and Research Epidemiology, Henry Ford Hospital, Detroit, Michigan, United States of America
| | | | - Pamela J. Schreiner
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Lisa B. Signorello
- International Epidemiology Institute, Rockville, Maryland, United States of America
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt–Ingram Cancer Center, Nashville, Tennessee, United States of America
| | - Andrew B. Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Alex H. Stram
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Daniel O. Stram
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Sara S. Strom
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Bhoom Suktitipat
- Department of Medicine, The Johns Hopkins GeneSTAR Research Program, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Michael J. Thun
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, United States of America
| | - John S. Witte
- Institute for Human Genetics, Departments of Epidemiology and Biostatistics and Urology, University of California San Francisco, San Francisco, California, United States of America
| | - Lisa R. Yanek
- Department of Medicine, The Johns Hopkins GeneSTAR Research Program, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Regina G. Ziegler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt–Ingram Cancer Center, Nashville, Tennessee, United States of America
| | - Xiaofeng Zhu
- Department of Biostatistics and Epidemiology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Joseph M. Zmuda
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alan B. Zonderman
- Laboratory of Personality and Cognition, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Michele K. Evans
- Health Disparities Research Section, Clinical Research Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Yongmei Liu
- Sticht Center on Aging, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Diane M. Becker
- Department of Medicine, The Johns Hopkins GeneSTAR Research Program, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Richard S. Cooper
- Department of Preventive Medicine and Epidemiology, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois, United States of America
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Joel N. Hirschhorn
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Divisions of Genetics and Endocrinology and Program in Genomics, Children's Hospital Boston, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (JN Hirschhorn); (G Lettre); (CA Haiman)
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, Canada
- Département de Médecine, Université de Montréal, Montréal, Canada
- * E-mail: (JN Hirschhorn); (G Lettre); (CA Haiman)
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
- * E-mail: (JN Hirschhorn); (G Lettre); (CA Haiman)
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24
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Chen F, Chen GK, Millikan RC, John EM, Ambrosone CB, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Deming SL, Bandera EV, Nyante S, Palmer JR, Rebbeck TR, Ingles SA, Press MF, Rodriguez-Gil JL, Chanock SJ, Le Marchand L, Kolonel LN, Henderson BE, Stram DO, Haiman CA. Fine-mapping of breast cancer susceptibility loci characterizes genetic risk in African Americans. Hum Mol Genet 2011; 20:4491-503. [PMID: 21852243 DOI: 10.1093/hmg/ddr367] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genome-wide association studies (GWAS) have revealed 19 common genetic variants that are associated with breast cancer risk. Testing of the index signals found through GWAS and fine-mapping of each locus in diverse populations will be necessary for characterizing the role of these risk regions in contributing to inherited susceptibility. In this large study of breast cancer in African-American women (3016 cases and 2745 controls), we tested the 19 known risk variants identified by GWAS and replicated associations (P < 0.05) with only 4 variants. Through fine-mapping, we identified markers in four regions that better capture the association with breast cancer risk in African Americans as defined by the index signal (2q35, 5q11, 10q26 and 19p13). We also identified statistically significant associations with markers in four separate regions (8q24, 10q22, 11q13 and 16q12) that are independent of the index signals and may represent putative novel risk variants. In aggregate, the more informative markers found in the study enhance the association of these risk regions with breast cancer in African Americans [per allele odds ratio (OR) = 1.18, P = 2.8 × 10(-24) versus OR = 1.04, P = 6.1 × 10(-5)]. In this detailed analysis of the known breast cancer risk loci, we have validated and improved upon markers of risk that better characterize their association with breast cancer in women of African ancestry.
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Affiliation(s)
- Fang Chen
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
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25
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Hinch AG, Tandon A, Patterson N, Song Y, Rohland N, Palmer CD, Chen GK, Wang K, Buxbaum SG, Akylbekova EL, Aldrich MC, Ambrosone CB, Amos C, Bandera EV, Berndt SI, Bernstein L, Blot WJ, Bock CH, Boerwinkle E, Cai Q, Caporaso N, Casey G, Cupples LA, Deming SL, Diver WR, Divers J, Fornage M, Gillanders EM, Glessner J, Harris CC, Hu JJ, Ingles SA, Isaacs W, John EM, Kao WHL, Keating B, Kittles RA, Kolonel LN, Larkin E, Le Marchand L, McNeill LH, Millikan RC, Murphy A, Musani S, Neslund-Dudas C, Nyante S, Papanicolaou GJ, Press MF, Psaty BM, Reiner AP, Rich SS, Rodriguez-Gil JL, Rotter JI, Rybicki BA, Schwartz AG, Signorello LB, Spitz M, Strom SS, Thun MJ, Tucker MA, Wang Z, Wiencke JK, Witte JS, Wrensch M, Wu X, Yamamura Y, Zanetti KA, Zheng W, Ziegler RG, Zhu X, Redline S, Hirschhorn JN, Henderson BE, Taylor HA, Price AL, Hakonarson H, Chanock SJ, Haiman CA, Wilson JG, Reich D, Myers SR. The landscape of recombination in African Americans. Nature 2011; 476:170-5. [PMID: 21775986 PMCID: PMC3154982 DOI: 10.1038/nature10336] [Citation(s) in RCA: 230] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 06/27/2011] [Indexed: 01/14/2023]
Abstract
Recombination, together with mutation, gives rise to genetic variation in populations. Here we leverage the recent mixture of people of African and European ancestry in the Americas to build a genetic map measuring the probability of crossing over at each position in the genome, based on about 2.1 million crossovers in 30,000 unrelated African Americans. At intervals of more than three megabases it is nearly identical to a map built in Europeans. At finer scales it differs significantly, and we identify about 2,500 recombination hotspots that are active in people of West African ancestry but nearly inactive in Europeans. The probability of a crossover at these hotspots is almost fully controlled by the alleles an individual carries at PRDM9 (P value < 10(-245)). We identify a 17-base-pair DNA sequence motif that is enriched in these hotspots, and is an excellent match to the predicted binding target of PRDM9 alleles common in West Africans and rare in Europeans. Sites of this motif are predicted to be risk loci for disease-causing genomic rearrangements in individuals carrying these alleles. More generally, this map provides a resource for research in human genetic variation and evolution.
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Affiliation(s)
- Anjali G Hinch
- Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK
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26
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Millikan RC, Newman B, Tse CK, Moorman PG, Conway K, Dressler LG, Smith LV, Labbok MH, Geradts J, Bensen JT, Jackson S, Nyante S, Livasy C, Carey L, Earp HS, Perou CM. Epidemiology of basal-like breast cancer. Breast Cancer Res Treat 2007; 109:123-39. [PMID: 17578664 PMCID: PMC2443103 DOI: 10.1007/s10549-007-9632-6] [Citation(s) in RCA: 565] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2007] [Accepted: 05/24/2007] [Indexed: 12/29/2022]
Abstract
Risk factors for the newly identified "intrinsic" breast cancer subtypes (luminal A, luminal B, basal-like and human epidermal growth factor receptor 2-positive/estrogen receptor-negative) were determined in the Carolina Breast Cancer Study, a population-based, case-control study of African-American and white women. Immunohistochemical markers were used to subtype 1,424 cases of invasive and in situ breast cancer, and case subtypes were compared to 2,022 controls. Luminal A, the most common subtype, exhibited risk factors typically reported for breast cancer in previous studies, including inverse associations for increased parity and younger age at first full-term pregnancy. Basal-like cases exhibited several associations that were opposite to those observed for luminal A, including increased risk for parity and younger age at first term full-term pregnancy. Longer duration breastfeeding, increasing number of children breastfed, and increasing number of months breastfeeding per child were each associated with reduced risk of basal-like breast cancer, but not luminal A. Women with multiple live births who did not breastfeed and women who used medications to suppress lactation were at increased risk of basal-like, but not luminal A, breast cancer. Elevated waist-hip ratio was associated with increased risk of luminal A in postmenopausal women, and increased risk of basal-like breast cancer in pre- and postmenopausal women. The prevalence of basal-like breast cancer was highest among premenopausal African-American women, who also showed the highest prevalence of basal-like risk factors. Among younger African-American women, we estimate that up to 68% of basal-like breast cancer could be prevented by promoting breastfeeding and reducing abdominal adiposity.
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Affiliation(s)
- Robert C Millikan
- Department of Epidemiology, CB #7435, School of Public Health, University of North Carolina, Chapel Hill, NC 27599-7435, USA.
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27
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Livasy CA, Perou CM, Karaca G, Cowan DW, Maia D, Jackson S, Tse CK, Nyante S, Millikan RC. Identification of a basal-like subtype of breast ductal carcinoma in situ. Hum Pathol 2007; 38:197-204. [PMID: 17234468 DOI: 10.1016/j.humpath.2006.08.017] [Citation(s) in RCA: 160] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2006] [Revised: 08/23/2006] [Accepted: 08/24/2006] [Indexed: 02/02/2023]
Abstract
Microarray profiling of invasive breast carcinomas has identified subtypes including luminal A, luminal B, HER2-overexpressing, and basal-like. The poor-prognosis, basal-like tumors have been immunohistochemically characterized as estrogen receptor (ER)-negative, HER2/neu-negative, and cytokeratin 5/6-positive and/or epidermal growth factor receptor (EGFR)-positive. The aim of this study was to determine the prevalence of basal-like ductal carcinoma in situ in a population-based series of cases using immunohistochemical surrogates. A total of 245 pure ductal carcinoma in situ cases from a population-based, case-control study were evaluated for histologic characteristics and immunostained for ER, HER2/neu, EGFR, cytokeratin 5/6, p53, and Ki-67. The subtypes were defined as: luminal A (ER+, HER2-), luminal B (ER+, HER2+), HER2 positive (ER-, HER2+), and basal-like (ER-, HER2-, EGFR+, and/or cytokeratin 5/6+). The prevalence of breast cancer subtypes was basal-like (n = 19 [8%]); luminal A, n = 149 (61%); luminal B, n = 23 (9%); and HER2+/ER-, n = 38 (16%). Sixteen tumors (6%) were unclassified (negative for all 4 defining markers). The basal-like subtype was associated with unfavorable prognostic variables including high-grade nuclei (P < .0001), p53 overexpression (P < .0001), and elevated Ki-67 index (P < .0001). These studies demonstrate the presence of a basal-like in situ carcinoma, a potential precursor lesion to invasive basal-like carcinoma.
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Affiliation(s)
- Chad A Livasy
- Department of Pathology and Lab Medicine, University of North Carolina, Chapel Hill, NC 27599-7525, USA.
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Devries S, Nyante S, Korkola J, Segraves R, Nakao K, Moore D, Bae H, Wilhelm M, Hwang S, Waldman F. Array-based comparative genomic hybridization from formalin-fixed, paraffin-embedded breast tumors. J Mol Diagn 2005; 7:65-71. [PMID: 15681476 PMCID: PMC1867501 DOI: 10.1016/s1525-1578(10)60010-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Identification of prognostic and predictive genomic markers requires long-term clinical follow-up of patients. Extraction of high-quality DNA from archived formalin-fixed, paraffin-embedded material is essential for such studies. Of particular importance is a robust reproducible method of whole genome amplification for small tissue samples. This is especially true for high-resolution analytical approaches because different genomic regions and sequences may amplify differentially. We have tested a number of protocols for DNA amplification for array-based comparative genomic hybridization (CGH), in which relative copy number of the entire genome is measured at 1 to 2 mb resolution. Both random-primed amplification and degenerate oligonucleotide-primed amplification approaches were tested using varying amounts of fresh and paraffin-extracted normal and breast tumor input DNAs. We found that random-primed amplification was clearly superior to degenerate oligonucleotide-primed amplification for array-based CGH. The best quality and reproducibility strongly depended on accurate determination of the amount of input DNA using a quantitative polymerase chain reaction-based method. Reproducible and high-quality results were attained using 50 ng of input DNA, and some samples yielded quality results with as little as 5 ng input DNA. We conclude that random-primed amplification of DNA isolated from paraffin sections is a robust and reproducible approach for array-based CGH analysis of archival tumor samples.
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Affiliation(s)
- Sandy Devries
- Cancer Center, Box 0808, University of California San Francisco, San Francisco, CA 94143-0808, USA
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